diff --git a/packages/backend/server/src/prelude.ts b/packages/backend/server/src/prelude.ts
index 193a9468200d2..49191969e89aa 100644
--- a/packages/backend/server/src/prelude.ts
+++ b/packages/backend/server/src/prelude.ts
@@ -1,7 +1,7 @@
 import 'reflect-metadata';
 
 import { cpSync } from 'node:fs';
-import { join } from 'node:path';
+import { join, parse } from 'node:path';
 import { fileURLToPath, pathToFileURL } from 'node:url';
 
 import { config } from 'dotenv';
@@ -12,20 +12,28 @@ import {
 } from './fundamentals/config';
 import { enablePlugin } from './plugins';
 
-const configDir = join(fileURLToPath(import.meta.url), '../config');
+const PROJECT_CONFIG_PATH = join(fileURLToPath(import.meta.url), '../config');
 async function loadRemote(remoteDir: string, file: string) {
-  const filePath = join(configDir, file);
-  if (configDir !== remoteDir) {
-    cpSync(join(remoteDir, file), filePath, {
+  let fileToLoad = join(PROJECT_CONFIG_PATH, file);
+
+  if (PROJECT_CONFIG_PATH !== remoteDir) {
+    const remoteFile = join(remoteDir, file);
+    const remoteFileAtLocal = join(
+      PROJECT_CONFIG_PATH,
+      parse(file).name + '.remote.js'
+    );
+    cpSync(remoteFile, remoteFileAtLocal, {
       force: true,
     });
+    fileToLoad = remoteFileAtLocal;
   }
 
-  await import(pathToFileURL(filePath).href);
+  await import(pathToFileURL(fileToLoad).href);
 }
 
 async function load() {
-  const AFFiNE_CONFIG_PATH = process.env.AFFINE_CONFIG_PATH ?? configDir;
+  const AFFiNE_CONFIG_PATH =
+    process.env.AFFINE_CONFIG_PATH ?? PROJECT_CONFIG_PATH;
   // Initializing AFFiNE config
   //
   // 1. load dotenv file to `process.env`
@@ -44,15 +52,22 @@ async function load() {
   // TODO(@forehalo):
   //   Modules may contribute to ENV_MAP, figure out a good way to involve them instead of hardcoding in `./config/affine.env`
   // 3. load env => config map to `globalThis.AFFiNE.ENV_MAP
+  // load local env map as well in case there are new env added
+  await loadRemote(PROJECT_CONFIG_PATH, 'affine.env.js');
+  const projectEnvMap = AFFiNE.ENV_MAP;
   await loadRemote(AFFiNE_CONFIG_PATH, 'affine.env.js');
+  const customEnvMap = AFFiNE.ENV_MAP;
+  AFFiNE.ENV_MAP = { ...projectEnvMap, ...customEnvMap };
 
   // 4. load `config/affine` to patch custom configs
+  // load local config as well in case there are new default configurations added
+  await loadRemote(PROJECT_CONFIG_PATH, 'affine.js');
   await loadRemote(AFFiNE_CONFIG_PATH, 'affine.js');
 
   // 5. load `config/affine.self` to patch custom configs
   // This is the file only take effect in [AFFiNE Cloud]
   if (!AFFiNE.isSelfhosted) {
-    await loadRemote(AFFiNE_CONFIG_PATH, 'affine.self.js');
+    await loadRemote(PROJECT_CONFIG_PATH, 'affine.self.js');
   }
 
   // 6. apply `process.env` map overriding to `globalThis.AFFiNE`