diff --git a/rdagent/app/cli.py b/rdagent/app/cli.py
index 154023d3..0f3411a3 100644
--- a/rdagent/app/cli.py
+++ b/rdagent/app/cli.py
@@ -5,11 +5,16 @@ This will
 - make rdagent a nice entry and
 - autoamtically load dotenv
 """
+from dotenv import load_dotenv
+
+load_dotenv(".env")
+# 1) Make sure it is at the beginning of the script so that it will load dotenv before initializing BaseSettings.
+# 2) The ".env" argument is necessary to make sure it loads `.env` from the current directory.
+
 import subprocess
 from importlib.resources import path as rpath
 
 import fire
-from dotenv import load_dotenv
 
 from rdagent.app.data_mining.model import main as med_model
 from rdagent.app.general_model.general_model import (
@@ -20,8 +25,6 @@ from rdagent.app.qlib_rd_loop.factor_from_report import main as fin_factor_repor
 from rdagent.app.qlib_rd_loop.model import main as fin_model
 from rdagent.app.utils.info import collect_info
 
-load_dotenv()
-
 
 def ui(port=80, log_dir="", debug=False):
     """
diff --git a/rdagent/app/general_model/general_model.py b/rdagent/app/general_model/general_model.py
index cb05dd50..5da2c5a9 100644
--- a/rdagent/app/general_model/general_model.py
+++ b/rdagent/app/general_model/general_model.py
@@ -1,9 +1,3 @@
-from dotenv import load_dotenv
-
-from rdagent.scenarios.general_model.scenario import GeneralModelScenario
-
-load_dotenv(override=True)
-
 import fire
 
 from rdagent.components.coder.model_coder.task_loader import (
@@ -13,6 +7,7 @@ from rdagent.components.document_reader.document_reader import (
     extract_first_page_screenshot_from_pdf,
 )
 from rdagent.log import rdagent_logger as logger
+from rdagent.scenarios.general_model.scenario import GeneralModelScenario
 from rdagent.scenarios.qlib.developer.model_coder import QlibModelCoSTEER
 
 
diff --git a/rdagent/components/benchmark/conf.py b/rdagent/components/benchmark/conf.py
index 095212a7..0a0ad418 100644
--- a/rdagent/components/benchmark/conf.py
+++ b/rdagent/components/benchmark/conf.py
@@ -2,13 +2,8 @@ from dataclasses import field
 from pathlib import Path
 from typing import Optional
 
-from dotenv import load_dotenv
 from pydantic_settings import BaseSettings
 
-# Load environment variables
-load_dotenv(verbose=True, override=True)
-
-
 DIRNAME = Path("./")
 
 
diff --git a/rdagent/components/runner/conf.py b/rdagent/components/runner/conf.py
index e7670ace..1791dde7 100644
--- a/rdagent/components/runner/conf.py
+++ b/rdagent/components/runner/conf.py
@@ -2,12 +2,6 @@ from __future__ import annotations
 
 from pathlib import Path
 
-from dotenv import load_dotenv
-from pydantic_settings import BaseSettings
-
-# make sure that env variable is loaded while calling Config()
-load_dotenv(verbose=True, override=True)
-
 from pydantic_settings import BaseSettings
 
 
diff --git a/rdagent/core/conf.py b/rdagent/core/conf.py
index 202ac1ea..6d193c7d 100644
--- a/rdagent/core/conf.py
+++ b/rdagent/core/conf.py
@@ -2,15 +2,11 @@ from __future__ import annotations
 
 from pathlib import Path
 
-from dotenv import load_dotenv
 from pydantic_settings import BaseSettings
 
 # TODO: use pydantic for other modules in Qlib
 # from pydantic_settings import BaseSettings
 
-# make sure that env variable is loaded while calling Config()
-load_dotenv(verbose=True, override=True)
-
 
 class RDAgentSettings(BaseSettings):
     # TODO: (xiao) I think LLMSetting may be a better name.