During pregnancy the cervix softens due to hormones, and your labias/vulva swell due to the increased blood flow.
If he is doing deep thrusting he could be hitting your cervix, which can be painful even when not pregnant. I have noticed within myself my upper vaginal wall is also tender at times due to the pressure and stretching from the baby laying on it. Try putting a pillow, or two, under your butt during sex. This will help to give him optimal position when thrusting so that he doesn't hit your cervix.
If the pain is in the labias/vulva it could be due to swelling. In this case you can try using ice packs to help with the swelling. During sex you want to find a position where he doesn't bump, or rub, against the labias/vulva. Try sex standing up with him behind you, or doggy style.