diff --git a/src/core/config.ts b/src/core/config.ts
index 77831fd..2da0444 100644
--- a/src/core/config.ts
+++ b/src/core/config.ts
@@ -94,6 +94,10 @@ function mergeConfig(userConfig: Partial<RuneConfig>): RuneConfig {
     }
   }
 
+  if (userConfig.metadata) {
+    result.metadata = userConfig.metadata;
+  }
+
   return result;
 }
 
diff --git a/tests/core/config.test.ts b/tests/core/config.test.ts
index fc2b90b..6f040c9 100644
--- a/tests/core/config.test.ts
+++ b/tests/core/config.test.ts
@@ -170,3 +170,38 @@ describe("validateConfig", () => {
     expect(() => validateConfig(config)).not.toThrow();
   });
 });
+
+describe("mergeConfig 保留 metadata", () => {
+  it("保留用户配置中的 metadata", async () => {
+    const tmpDir = join(import.meta.dir, "__tmp_config_meta_test__");
+    await mkdir(tmpDir, { recursive: true });
+    try {
+      const configPath = join(tmpDir, ".rune", "config.yaml");
+      await mkdir(join(tmpDir, ".rune"), { recursive: true });
+      await writeFile(
+        configPath,
+        `metadata:\n  command: "bunx @lanyuanxiaoyao/rune"\nstages:\n  discuss:\n    prompt: "自定义讨论"\n`,
+      );
+      const config = await loadConfig(tmpDir);
+      expect(config.metadata).toBeDefined();
+      expect(config.metadata!.command).toBe("bunx @lanyuanxiaoyao/rune");
+      expect(config.stages.discuss!.prompt).toBe("自定义讨论");
+    } finally {
+      await rm(tmpDir, { recursive: true, force: true });
+    }
+  });
+
+  it("无 metadata 时不设置该字段", async () => {
+    const tmpDir = join(import.meta.dir, "__tmp_config_nometa_test__");
+    await mkdir(tmpDir, { recursive: true });
+    try {
+      const configPath = join(tmpDir, ".rune", "config.yaml");
+      await mkdir(join(tmpDir, ".rune"), { recursive: true });
+      await writeFile(configPath, `stages:\n  discuss:\n    prompt: "测试"\n`);
+      const config = await loadConfig(tmpDir);
+      expect(config.metadata).toBeUndefined();
+    } finally {
+      await rm(tmpDir, { recursive: true, force: true });
+    }
+  });
+});