How important are undergraduate and masters studies transcripts in applying for a faculty position? I am going to apply for a faculty position via online system. In the announcement of the position  they have just asked for cover letter, contact info of references and C.V. But in the online process of application I noticed that there exists some taps related to uploading transcripts of B.Sc, M.Sc and Ph.D. I do not know whether they need transcripts or not? Can a bad transcript have bad effect on applying for a a faculty position?
I do not know whether they need transcripts or not?

There are two slightly orthogonal aspects when you apply to faculty positions:

What the panel will use to determine if they will offer an interview,
What the administration requires for your application to be complete.

The announcement will focus on 1., but when actually applying, you may realize that 2. is a bit different.
If the application platform requires your transcripts, upload them, and don't think too much about them: they may or may not be reviewed by the panel, but what you did during your PhD and your cover letter will have a greater weight than those transcripts.
If the application platform does not require the transcripts, then I guess it's up to you. You can probably just upload them later on if the panel would like to have a look at it, but as Bill Barth noted in the comment, that is probably not a good idea to give the panel a possible reason to filter out your application before even looking at it.

Can a bad transcript have bad effect on applying for a a faculty position?

As I wrote, they can, but whether they will depends on multiple factors that are hard to assess. I believe it is reasonably safe to say that your PhD, cover letter, and possibly letter(s) of recommendation will have a greater weight, but that does not necessarily imply that your transcript will have a zero weight.
Good luck, I hope your application will receive favorable reviews!