OK, thanks for pointing me to procmon, actually I used it before but didn't think of it at the first time.
I've tried to run devenv.exe with Administrator user but it didn't work, and procmon reveals that when devenv.exe reads HKCR\.pyproj it got ACCESS DENIED.
When I check the permission of that key with regedit.exe with administrator permission I even can't change its permission. weird. But seems it's not Python Tools' problem. I'll post an update after I got some progress.