Unless you explicitly require GitPython for 'plumbing', it is recommended to use Repo(path).git.add(…, chmod='+x'), which supports all flags that git supports. You can read more about that in the respective section of the docs.

Even though I am closing this issue assuming you don't actually need plumbing, please let me know if you do which would make this a feature request or bugfix. Thank you

Thank you Byron. I actually used the repo.git.add as a solution and it works well. I was just thinking index.add is more like a native solution for GitPython and expect to be as versatile as git shell command. Up to you to judge :)