When slapping, my third finger knuckle hurts
 

I slap in a conventional manner - make a fist, stick the thumb out and slap. When I slap, my third finger knuckle frequently hits the body of the bass (especially when slapping fast). After a while, it hurts. Does anyone have this problem?

When slapping , I really don't hit the strings very hard at all so whilst the knuckle does touch the top of the instrument at times it does not do so hard enough for any pain to be caused.
It's a matter of being relaxed and free whilst playing I guess.

Disclaimer: I am NOT an expert/master at slap/pop

Are you practicing through an amp? It's much better to slap/pop through an amp than doing it acoustically on your couch. You won't have to be as aggressive.

It could also be technique. Slapping should have the similar wrist motion as turning a door knob. When you pop, I think your hand should float a bit and you shouldn't use your ring/pinky knuckle against the body as leverage. Palm muting could help keep your knuckle off the body.

I don't use my middle finger as a leverage. And I move only my wrist to slap.

I recently got into slap, so my skill is terrible.

I guess I slap too aggressively. Also, I frequently practice without an amp at home. So I guess I subconsciously slap even harder.

I've always done it from the wrist. My arm and wrist stay in one spot, and turning from the wrist gives the slap, not a striking motion with the whole arm. This also puts your other fingers in perfect position for the pull.