diff --git a/src/app/service/content/utils.test.ts b/src/app/service/content/utils.test.ts
index e4bf62ed9..468ef94fe 100644
--- a/src/app/service/content/utils.test.ts
+++ b/src/app/service/content/utils.test.ts
@@ -214,9 +214,27 @@ describe("utils", () => {
 
       expect(result).toBeDefined();
       expect(result).toContain(
-        `GM_registerMenuCommand(("ScriptCat's demo for \\"context-menu\\""), ()=>{let GM_registerMenuCommand=window.GM_registerMenuCommand=GM.registerMenuCommand=undefined;\nconsole.log(567); // testing\n}, {nested:false});\n`
+        `GM_registerMenuCommand(("ScriptCat's demo for \\"context-menu\\""), ()=>{\nconsole.log(567); // testing\n}, {nested:false});\n`
       );
     });
+
+    it.concurrent("@run-at context-menu 的包装不得屏蔽脚本体自己的 GM_registerMenuCommand", () => {
+      const scriptRes = createMockScriptRes({
+        name: "menu registering script",
+        code: 'GM_registerMenuCommand("Own Item", () => {});',
+        metadata: {
+          "run-at": ["context-menu"],
+        },
+      });
+
+      const result = compileScriptCode(scriptRes);
+
+      // 曾经在回调开头把 GM_registerMenuCommand 连同 window./GM. 上的引用一起置为 undefined，
+      // 于是任何在脚本体里注册菜单的脚本一点菜单就 TypeError 中断，自己的菜单项也永远注册不上
+      expect(result).not.toContain("GM_registerMenuCommand=undefined");
+      expect(result).not.toContain("window.GM_registerMenuCommand");
+      expect(result).not.toContain("GM.registerMenuCommand");
+    });
   });
 
   describe("compileScript", () => {
diff --git a/src/app/service/content/utils.ts b/src/app/service/content/utils.ts
index bc7905a0b..8f464773d 100644
--- a/src/app/service/content/utils.ts
+++ b/src/app/service/content/utils.ts
@@ -141,7 +141,8 @@ export function compileScriptCodeByResource(resource: CompileScriptCodeResource)
   // 在UserScripts API中，由于执行不是在物件导向里呼叫，使用arrow function的话会把this改变。须使用 .call(this) [ 或 .bind(this)() ]
 
   if (resource.isContextMenu) {
-    code = `GM_registerMenuCommand((${JSON.stringify(resource.name)}), ()=>{let GM_registerMenuCommand=window.GM_registerMenuCommand=GM.registerMenuCommand=undefined;\n${code}\n}, {nested:false});\n`;
+    // 脚本体整体延后到菜单回调里执行，它自己的 GM_registerMenuCommand 也随之推迟到点击后才注册
+    code = `GM_registerMenuCommand((${JSON.stringify(resource.name)}), ()=>{\n${code}\n}, {nested:false});\n`;
   }
 
   const joinedCode = [
diff --git a/src/app/service/service_worker/gm_api/gm_api.ts b/src/app/service/service_worker/gm_api/gm_api.ts
index 36d0c6eed..853ebc3aa 100644
--- a/src/app/service/service_worker/gm_api/gm_api.ts
+++ b/src/app/service/service_worker/gm_api/gm_api.ts
@@ -36,7 +36,7 @@ import type {
 } from "../types";
 import type { TScriptMenuRegister, TScriptMenuUnregister } from "../../queue";
 import type { NotificationOptionCache } from "../utils";
-import { BrowserNoSupport, notificationsUpdate } from "../utils";
+import { BrowserNoSupport, getCombinedMeta, notificationsUpdate } from "../utils";
 import {
   getSkillScriptGrantsByUuid,
   getSkillScriptNameByUuid,
@@ -416,6 +416,10 @@ export default class GMApi {
       if (!script) {
         throw new Error("script is not found");
       }
+      // 设置面板改的运行时机等只写 selfMetadata，GM API 校验要看合并后的生效值（#1649）
+      if (script.selfMetadata) {
+        script = { ...script, metadata: getCombinedMeta(script.metadata, script.selfMetadata) };
+      }
     }
     // 订阅脚本的 connect 使用订阅声明的 connect 覆盖脚本自身的
     if (script.subscribeUrl) {
diff --git a/src/app/service/service_worker/gm_api/gm_api_self_metadata.test.ts b/src/app/service/service_worker/gm_api/gm_api_self_metadata.test.ts
new file mode 100644
index 000000000..d8b3f9ab4
--- /dev/null
+++ b/src/app/service/service_worker/gm_api/gm_api_self_metadata.test.ts
@@ -0,0 +1,81 @@
+import { describe, it, expect, beforeEach } from "vitest";
+import { ScriptDAO, SCRIPT_TYPE_NORMAL, SCRIPT_STATUS_ENABLE, SCRIPT_RUN_STATUS_COMPLETE } from "@App/app/repo/scripts";
+import type { Script } from "@App/app/repo/scripts";
+import GMApi, { MockGMExternalDependencies } from "./gm_api";
+import { initTestEnv } from "@Tests/utils";
+import { MockMessage } from "@Packages/message/mock_message";
+import { Server, type IGetSender } from "@Packages/message/server";
+import type { ExtMessageSender } from "@Packages/message/types";
+import EventEmitter from "eventemitter3";
+import { MessageQueue } from "@Packages/message/message_queue";
+import { SystemConfig } from "@App/pkg/config/config";
+import PermissionVerify, { PermissionVerifyApiGet } from "../permission_verify";
+import type { ValueService } from "../value";
+
+initTestEnv();
+
+const makeSender = (): IGetSender => ({
+  getSender: () => ({}) as chrome.runtime.MessageSender,
+  getType: () => 0,
+  isType: (_type: any) => false,
+  getExtMessageSender: () => null as unknown as ExtMessageSender,
+  getConnect: () => undefined,
+});
+
+const createGMApi = () => {
+  const ee = new EventEmitter<string, any>();
+  const message = new MockMessage(ee);
+  const messageQueue = new MessageQueue();
+  const systemConfig = new SystemConfig(messageQueue);
+  const server = new Server("serviceWorker", message);
+  const permissionVerify = new PermissionVerify(server.group("permissionVerify"), messageQueue);
+  const gmApi = new GMApi(
+    systemConfig,
+    permissionVerify,
+    server.group("runtime"),
+    message,
+    messageQueue,
+    {} as ValueService,
+    new MockGMExternalDependencies()
+  );
+  return { gmApi, permissionVerify };
+};
+
+// 设置面板把运行时机改成 context-menu 只写 selfMetadata，脚本自带 metadata 不变；
+// GM API 请求若只带自带 metadata，免 @grant 的菜单豁免就判不出来，菜单项注册不上（#1649）。
+describe("parseRequest 用户覆写的 metadata", () => {
+  let scriptDAO: ScriptDAO;
+
+  beforeEach(() => {
+    scriptDAO = new ScriptDAO();
+  });
+
+  it("selfMetadata 覆写 run-at=context-menu 的脚本，GM_registerMenuCommand 无需 @grant 即可通过校验", async () => {
+    const script: Script = {
+      uuid: "uuid-context-menu-override",
+      name: "test-script",
+      namespace: "test",
+      metadata: { grant: ["none"], "run-at": ["document-idle"] },
+      selfMetadata: { "run-at": ["context-menu"] },
+      type: SCRIPT_TYPE_NORMAL,
+      status: SCRIPT_STATUS_ENABLE,
+      sort: 0,
+      runStatus: SCRIPT_RUN_STATUS_COMPLETE,
+      createtime: Date.now(),
+      checktime: Date.now(),
+    };
+    await scriptDAO.save(script);
+    const { gmApi, permissionVerify } = createGMApi();
+
+    const req = await gmApi.parseRequest({
+      uuid: script.uuid,
+      api: "GM_registerMenuCommand",
+      runFlag: "",
+      params: [],
+    });
+
+    await expect(
+      permissionVerify.verify(req, PermissionVerifyApiGet("GM_registerMenuCommand")!, makeSender(), gmApi)
+    ).resolves.toBe(true);
+  });
+});
diff --git a/src/app/service/service_worker/runtime.test.ts b/src/app/service/service_worker/runtime.test.ts
index 27103b47c..cf4cc9c42 100644
--- a/src/app/service/service_worker/runtime.test.ts
+++ b/src/app/service/service_worker/runtime.test.ts
@@ -1192,3 +1192,83 @@ describe("MQ 事件处理效果（enableScripts / deleteScripts / sortedScripts
     expect((runtime as any).cachedPatterns.has(uuid)).toBe(false);
   });
 });
+
+// ─────────────────────────────────────────────────────────────────────────────
+
+describe("restoreJSCodeFromCompiledResource 还原代码时的生效 metadata", () => {
+  // 设置面板改运行时机只写 selfMetadata，脚本自带 metadata 原封不动；
+  // 还原路径若只看自带 metadata，重新注册后用户覆写就会静默失效（#1649）。
+  const createContext = (script: Script) => {
+    const { runtime, mockScriptService } = _createRuntimeContext();
+    const scriptRes = _createScriptRunResource(script);
+    const compiledResource: CompiledResource = {
+      name: script.name,
+      flag: `#-${script.uuid}`,
+      uuid: script.uuid,
+      require: [],
+      matches: ["https://www.example.com/*"],
+      includeGlobs: [],
+      excludeMatches: [],
+      excludeGlobs: [],
+      allFrames: false,
+      world: "MAIN",
+      runAt: "document_idle",
+      scriptUrlPatterns: scriptURLPatternResults(scriptRes)!.scriptUrlPatterns,
+      originalUrlPatterns: null,
+    };
+    mockScriptService.buildScriptRunResource.mockResolvedValue(scriptRes);
+    (runtime as any).script = {
+      ...mockScriptService,
+      scriptCodeDAO: { get: vi.fn().mockResolvedValue({ code: "console.log(1);" }) },
+    };
+    (runtime as any).resource = { resourceDAO: { get: vi.fn().mockResolvedValue(undefined) } };
+    return { runtime, compiledResource };
+  };
+
+  it("selfMetadata 覆写 run-at=context-menu 时，还原的代码应包裹 GM_registerMenuCommand", async () => {
+    const script = _createMockScript({
+      metadata: { match: ["https://www.example.com/*"], "run-at": ["document-idle"] },
+      selfMetadata: { "run-at": ["context-menu"] },
+    });
+    const { runtime, compiledResource } = createContext(script);
+
+    const code = await runtime.restoreJSCodeFromCompiledResource(script, compiledResource);
+
+    expect(code).toContain("GM_registerMenuCommand");
+  });
+
+  it("selfMetadata 覆写为 early-start 时，还原的代码应走预注入编译", async () => {
+    const script = _createMockScript({
+      metadata: { match: ["https://www.example.com/*"], "run-at": ["document-idle"] },
+      selfMetadata: { "early-start": [""], "run-at": ["document-start"] },
+    });
+    const { runtime, compiledResource } = createContext(script);
+
+    const code = await runtime.restoreJSCodeFromCompiledResource(script, compiledResource);
+
+    expect(code).toContain("performance.dispatchEvent");
+  });
+});
+
+describe("pushValueUpdate 判断是否需要为 early-start 脚本重新编译", () => {
+  // early-start 会把 GM 值编进预注入代码，值变了必须重编；
+  // 该脚本的 early-start 可能来自用户覆写，不能只看脚本自带 metadata。
+  it("selfMetadata 覆写为 early-start 的脚本，值更新后应重新编译注册", async () => {
+    const { runtime } = _createRuntimeContext();
+    const script = _createMockScript({
+      metadata: { match: ["https://www.example.com/*"], "run-at": ["document-idle"] },
+      selfMetadata: { "early-start": [""], "run-at": ["document-start"] },
+    });
+    const updateSpy = vi.spyOn(runtime, "updateResourceOnScriptChange").mockResolvedValue(undefined);
+
+    await runtime.pushValueUpdate(script, {
+      entries: [],
+      uuid: script.uuid,
+      storageName: "test-storage",
+      sender: { runFlag: "", tabId: -1 },
+      valueUpdated: true,
+    });
+
+    expect(updateSpy).toHaveBeenCalledWith(script);
+  });
+});
diff --git a/src/app/service/service_worker/runtime.ts b/src/app/service/service_worker/runtime.ts
index ca06143f1..4a33c67b8 100644
--- a/src/app/service/service_worker/runtime.ts
+++ b/src/app/service/service_worker/runtime.ts
@@ -13,6 +13,7 @@ import { runScript, stopScript } from "../offscreen/client";
 import {
   buildScriptRunResourceBasic,
   compileInjectionCode,
+  getCombinedMeta,
   getUserScriptRegister,
   parseUrlSRI,
   scriptURLPatternResults,
@@ -485,7 +486,10 @@ export class RuntimeService {
 
       // valueUpdate 消息用于 early script 的处理
       if (sendData.valueUpdated) {
-        if (script.status === SCRIPT_STATUS_ENABLE && isEarlyStartScript(script.metadata)) {
+        if (
+          script.status === SCRIPT_STATUS_ENABLE &&
+          isEarlyStartScript(getCombinedMeta(script.metadata, script.selfMetadata))
+        ) {
           // 如果是预加载脚本，需要更新脚本代码重新注册
           // scriptMatchInfo 里的 value 改变 => compileInjectionCode -> injectionCode 改变
           await this.updateResourceOnScriptChange(script);
@@ -902,15 +906,19 @@ export class RuntimeService {
 
   // 从CompiledResource中还原脚本代码
   async restoreJSCodeFromCompiledResource(script: Script, result: CompiledResource) {
+    // 用户在设置面板改运行时机只写 selfMetadata，脚本自带 metadata 不变，
+    // 所以编译分支必须按合并后的生效 metadata 选，否则重新注册会丢掉覆写（#1649）
+    const metadata = getCombinedMeta(script.metadata, script.selfMetadata);
+
     // 如果是 Scriptlet (unwrap) 脚本，需要另外的处理方式
-    if (isScriptletUnwrap(script.metadata)) {
+    if (isScriptletUnwrap(metadata)) {
       const scriptRes = await this.script.buildScriptRunResource(script);
       if (!scriptRes) return "";
       return compileScriptletCode(scriptRes, scriptRes.code, result.scriptUrlPatterns);
     }
 
     // 如果是预加载脚本，需要另外的处理方式
-    if (isEarlyStartScript(script.metadata)) {
+    if (isEarlyStartScript(metadata)) {
       const scriptRes = await this.script.buildScriptRunResource(script);
       if (!scriptRes) return "";
       return compileInjectionCode(scriptRes, scriptRes.code, result.scriptUrlPatterns);
@@ -931,7 +939,7 @@ export class RuntimeService {
         name: result.name,
         code: originalCode?.code || "",
         require,
-        isContextMenu: isContextMenuScript(script.metadata),
+        isContextMenu: isContextMenuScript(metadata),
       })
     );
   }
diff --git a/src/app/service/service_worker/utils.ts b/src/app/service/service_worker/utils.ts
index 753befa28..456013438 100644
--- a/src/app/service/service_worker/utils.ts
+++ b/src/app/service/service_worker/utils.ts
@@ -137,7 +137,7 @@ export async function notificationsUpdate(
   }
 }
 
-export function getCombinedMeta(metaBase: SCMetadata, metaCustom: SCMetadata): SCMetadata {
+export function getCombinedMeta(metaBase: SCMetadata, metaCustom: SCMetadata | undefined): SCMetadata {
   const metaRet = { ...metaBase };
   if (!metaCustom) {
     return metaRet;