As a dairy product, cheese is an excellent source of calcium to strengthen teeth and bones. It's pretty obvious that cheese pizza contains more calcium than pepperoni pizza. In fact, in one serving, a cheese pizza can provide up to 20% of the daily calcium intake of average human beings. Cheese pizza usually contains more calories and fat than pepperoni pizza.
This is due to the cheese itself, as well as the fact that cheese pizzas usually have a thicker dough.