A delicious red cherry is often placed on top of a cake or an ice cream dessert in order to make it even more appealing to the eye and the sense of taste.
So the "cherry on top" is the final touch that makes something as attractive as possible.
If you say "Pretty please with a cherry on top", it means you are trying to make your offer as attractive as possible. Children and desperate adults use this expression when every other attempt to persuade another person has failed.
A similar phrase is "Pretty please "with sugar on top". The idea is that putting sugar on top of something makes it more attractive.
Often the expressions "with sugar on top" and "with a cherry on top" are used sarcastically.
example:
Pretty please with a cherry on top, would you move your stupid car, it's blocking my driveway!