If your kitty has an accident in the car, it is time to get out your cleaning supplies. The smell of urine in a closed car can get very strong. This is a guide about removing cat urine smell from car interior.
How do you get cat pee scent out of the car on back of the seat?
Once you have cleaned the upholstery, spinkle baking soda on the dry upholstery and let it sit a few days. Then, when you can leave the car closed up for a day or two (especially if it will be sunny), pour some dry, unused coffee grounds into shallow dishes, and put them in the car, then close it up tightly; a day or two is great, if you can. Vacuum the baking soda, and let the car air out. Hopefully it will take care of it.
You might also check the pet store; they sell enzymatic products that you put on and let dry (like Febreeze), but that are specially formulated for pet urine.