Should I file for Green Card if parents were denied B2 visa a couple of times?

Yes, you can do the green card application on their behalf. However, this will take about 9-12 months. After that, once they visit, if they do not intend to reside permanently in the US but just use the green card to "visit" there is a good chance that they will lose it after a few visits if they are deemed not to be residing permanently in the US or at least have that intention.

The reasons why a U.S. consulate will deny someone a visitor visa depends in part on which country they are from. It does not help that you are a U.S. citizen as they will assume that your parents have the intent to live in the U.S. permanently. Since the visitor visa was denied more than once, it is not very likely that it will ever be issued. You do have the option of applying for green cards on their behalf and if at some point in the future, they wish to abandon that status, they can do so. So long as you remain a U.S. citizen, you can always refile for green cards for them at some point in the future.