What would happen if I applied for citizenship based on marriage and separated after would it affect my case?

You will have to disclose whether you separated or divorced. I've seen this type of thing before. So long as USCIS is satisfied that you had a bona fide marriage, you should be ok. I would take an attorney with you just to be on the safe side.

You need to disclose and explain all changes of your marital status honestly, especially if initial legal ground was hinged on that effected marriage. I would consult a counsel in person before proceeding.

Staying for citizenship isn't a reason to remain married but if your marriage has chance of reconciliation then by all means try to make it work. The CIS will review all information provided, whichuat be truthful and accurate. Please seek assistance of an experienced immigration attorney for consult and possible consequences to path towards citizenship.