I know exactly what you mean.
For me - I lost my virginity at a young age, and threw my body toward anyone who'd take it for a period of time. Whilst that can be a recipe for a fantastic sex-life, it wasn't for me at that time. I stopped associating sex with love, and when I got a long-term boyfriend, I would feel horrible after sex. Almost in a 'how could he do this to me'-way.
Maybe it's the same for you - I don't know how sex has been for you before your boyfriend. It could also be worth considering if you really are truly in love with him. I've seen that it's easy for people to fool themselves into thinking so, and I know sex can decrease in fun a LOT when love starts to fade.
Another option could be asexuality. It comes in many shapes and sizes - some people find sex absolutely repulsive and want nothing to do with it, whereas others don't mind sex, but just don't care to initiate it.Only you can really find the answer as to why sex makes you feel so uncomfortable. The most important thing to remember while figuring this out, is that it's okay. Whatever it is, it's fine. Do not ever beat yourself up over this. I know how easy it is to be hard on yourself on this subject, to a point of depression. But there's no reason to. You don't have to do anything you don't want to do.
And last, but not least, you should talk to your boyfriend about this. Tell him whatever you do know. If he were to leave you for that, he wouldn't be worth keeping to begin with.Best of luck. X!