I wanted to ask my friend what color his car is. It seems to me that there are two sentences for that. "what color is the car? "or "what is the color of the car?" Which one is correct? If both of them are correct, which one makes more sense to a native English speaker?
They are both correct.
The difference is the second one demonstrates the asker is interested specifically in the color of the car as more important then other characteristics. For example, if you car is stolen, the officier will ask "What is the color of the car?" since that is it's most identifying characteristic when looking for it.
If you are buying a car, you would ask "What color is the car? How big is the engine? Are the seats leather?" when color is one of many things you're interested in.
Both sentences are completely correct, and both sentences completely make sense. The sentence "What color is the car?" is probably a little bit better, because it's a little bit shorter.