I am the one who asks the question. In fact, the tool the closest to my needs seems to be PythonTidy (it's a Python program of course : Python is best served by himself ;) ).

autopep8

autopep8 would auto-format your python script. not only the code indentation, but also other coding spacing styles. It makes your python script to conform PEP8 Style Guide.

pip install autopep8
autopep8 your_script.py    # dry-run, only print
autopep8 -i your_script.py # replace content

Update:

Many editors have pep8 plugins that automatically reformat your code right after you save the file. py-autopep8 in emacs

yapf

yapf is a new and better python code formatter. which tries to get the best formatting, not just to conform the guidelines. The usage is quite the same as autopep8.

pip install yapf
yapf your_script.py    # dry-run, only print
yapf -i your_script.py # replace content

For more information, like formatting configurations, please read the README.rst on yapf github

Update 2:

Black

Black is much better than yapf. It's smarter and fits most complex formatting cases.