During sex can vagina hurt if I have hemriod in my butt....And we are having vagina sex only?

Yes. The space between the vaginal opening and the rectum varies but they can be quite close. With intercourse there is enough transmitted motion to the anus that a nearby hemorrhoid (varicose vein of the rectum) could be irritated and cause pain. Using a good lubricant might help but getting the hemorrhoid taken care of would be better.