diff --git a/scripts/pnpm-cli-resolver.mjs b/scripts/pnpm-cli-resolver.mjs
new file mode 100644
index 000000000..6a4d1bb38
--- /dev/null
+++ b/scripts/pnpm-cli-resolver.mjs
@@ -0,0 +1,37 @@
+// resolvePnpmCliPath 的独立模块：run-affected-unit-tests.mjs 顶层即执行 main()，
+// 无法被测试直接导入，这里抽出纯函数便于单测覆盖（scripts 测试走 node --test）。
+import { existsSync } from "node:fs";
+import { delimiter, join } from "node:path";
+
+// 候选会被 process.execPath 当作 JS 入口执行，只接受 JS 形态的文件：
+// mise 独立版 pnpm 的 npm_execpath 指向原生 pnpm.exe（MZ 头二进制），
+// 直接喂给 node 会以 SyntaxError 崩溃（#54），此时应回落到 PATH 搜索或 shell 兜底。
+const JS_ENTRY_PATH = /\.(?:cjs|mjs|js)$/iu;
+
+export function isJsEntryPath(file) {
+  return JS_ENTRY_PATH.test(file);
+}
+
+export function resolvePnpmCliPath(env) {
+  const npmExecPath = env.npm_execpath;
+  if (
+    npmExecPath &&
+    (npmExecPath.toLowerCase().includes("\\pnpm\\") || npmExecPath.toLowerCase().includes("/pnpm/")) &&
+    isJsEntryPath(npmExecPath)
+  ) {
+    return npmExecPath;
+  }
+
+  const pathEntries = (env.PATH ?? env.Path ?? "")
+    .split(delimiter)
+    .map((entry) => entry.trim())
+    .filter(Boolean);
+  for (const pathEntry of pathEntries) {
+    const candidate = join(pathEntry, "node_modules", "pnpm", "bin", "pnpm.cjs");
+    if (existsSync(candidate)) {
+      return candidate;
+    }
+  }
+
+  return undefined;
+}
diff --git a/scripts/pnpm-cli-resolver.test.mjs b/scripts/pnpm-cli-resolver.test.mjs
new file mode 100644
index 000000000..27bae30b2
--- /dev/null
+++ b/scripts/pnpm-cli-resolver.test.mjs
@@ -0,0 +1,48 @@
+import assert from "node:assert/strict";
+import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import test from "node:test";
+
+import { isJsEntryPath, resolvePnpmCliPath } from "./pnpm-cli-resolver.mjs";
+
+test("isJsEntryPath 只认 .cjs/.mjs/.js 形态", () => {
+  assert.equal(isJsEntryPath("tools/pnpm/bin/pnpm.cjs"), true);
+  assert.equal(isJsEntryPath("tools\\pnpm\\pnpm.mjs"), true);
+  assert.equal(isJsEntryPath("tools/pnpm/10.33.2/pnpm"), false);
+  assert.equal(isJsEntryPath("tools/pnpm/10.33.2/pnpm.EXE"), false);
+});
+
+test("npm_execpath 指向原生 pnpm.exe（mise 独立版）时不得作为 JS 入口候选", async () => {
+  const dir = await mkdtemp(join(tmpdir(), "pnpm-resolver-"));
+  try {
+    // join 的分隔符随平台变化，但两种形态都命中 npm_execpath 的 \pnpm\ / /pnpm/ 判定，
+    // 再由扩展名校验拒绝：这正是 #54 里 mise 独立版 pnpm 的实际形态。
+    const env = { npm_execpath: join(dir, "installs", "pnpm", "10.33.2", "pnpm.exe"), PATH: "" };
+    assert.equal(resolvePnpmCliPath(env), undefined);
+  } finally {
+    await rm(dir, { recursive: true, force: true });
+  }
+});
+
+test("npm_execpath 为 JS 形态时原样采用", () => {
+  const windowsStyle = { npm_execpath: "X:\\tools\\pnpm\\10.33.2\\pnpm.cjs", PATH: "" };
+  assert.equal(resolvePnpmCliPath(windowsStyle), windowsStyle.npm_execpath);
+  const posixStyle = { npm_execpath: "/home/dev/.local/share/pnpm/pnpm.cjs", PATH: "" };
+  assert.equal(resolvePnpmCliPath(posixStyle), posixStyle.npm_execpath);
+});
+
+test("npm_execpath 缺席或非法时回退 PATH 上的 node_modules/pnpm/bin/pnpm.cjs", async () => {
+  const dir = await mkdtemp(join(tmpdir(), "pnpm-resolver-"));
+  try {
+    const candidate = join(dir, "node_modules", "pnpm", "bin", "pnpm.cjs");
+    await mkdir(join(dir, "node_modules", "pnpm", "bin"), { recursive: true });
+    await writeFile(candidate, "// pnpm cli stub\n");
+
+    const withBadExecPath = { npm_execpath: join(dir, "pnpm.exe"), PATH: dir };
+    assert.equal(resolvePnpmCliPath(withBadExecPath), candidate);
+    assert.equal(resolvePnpmCliPath({ PATH: dir }), candidate);
+  } finally {
+    await rm(dir, { recursive: true, force: true });
+  }
+});
diff --git a/scripts/run-affected-unit-tests.mjs b/scripts/run-affected-unit-tests.mjs
index 109c5d8d9..728113ae8 100644
--- a/scripts/run-affected-unit-tests.mjs
+++ b/scripts/run-affected-unit-tests.mjs
@@ -3,9 +3,10 @@
 import { spawnSync } from "node:child_process";
 import { existsSync, mkdtempSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
-import { delimiter, join, resolve } from "node:path";
+import { join, resolve } from "node:path";
 
 import { selectDefaultBranchRef } from "./affected-unit-test-baseline.mjs";
+import { resolvePnpmCliPath } from "./pnpm-cli-resolver.mjs";
 
 const CODE_EXTENSIONS = new Set([
   ".cjs",
@@ -21,29 +22,6 @@ const CODE_EXTENSIONS = new Set([
 const CHANGED_DIFF_FILTER = "ACMRTUXB";
 const ZERO_SHA = /^0{40}$/u;
 
-function resolvePnpmCliPath(env) {
-  const npmExecPath = env.npm_execpath;
-  if (
-    npmExecPath &&
-    (npmExecPath.toLowerCase().includes("\\pnpm\\") || npmExecPath.toLowerCase().includes("/pnpm/"))
-  ) {
-    return npmExecPath;
-  }
-
-  const pathEntries = (env.PATH ?? env.Path ?? "")
-    .split(delimiter)
-    .map((entry) => entry.trim())
-    .filter(Boolean);
-  for (const pathEntry of pathEntries) {
-    const candidate = join(pathEntry, "node_modules", "pnpm", "bin", "pnpm.cjs");
-    if (existsSync(candidate)) {
-      return candidate;
-    }
-  }
-
-  return undefined;
-}
-
 function run(command, args, options = {}) {
   const spawnOptions = {
     cwd: options.cwd,