Hello Shin,
If you describe something as crap, you think that it is wrong or of very poor quality.
If you put up with something, you tolerate or accept it, even though you find it unpleasant or unsatisfactory.
So 'put up with crap' means tolerating and accepting things ,that you find wrong, unpleasant or unsatisfactory.
Example:
" He still loves her, although she always lies to him, why should he put up with all this crap?"