An ammonia smell in your litter box is bad, because it can discourage your cat from using its box. Arm and Hammer makes a great cat litter deodorizer product. You sprinkle some in the bottom of the box and then stir in some more every few days. Normal baking soda will absorb the odor as well.
You could switch to another litter, perhaps an unscented one. Or, if the ammonia smell is caused by soiled litter, cleaning it would eliminate the smell.
Try cleaning the box more often. Or by a pricier litter...the cheap clay stuff is always stinky. I have found that the "Tidy Cats Premium Scoop" works really well. Also, you can mix baking soda in with the litter. it helps absorb the odors.
You need to just dump out the entire litter box, wash it out and put in fresh litter. That ammonia smell is most likely coming from urine that has sunk down to the bottom of the box.