Abstract: How to charge for cloud computing is an important problem to be solved urgently at present.In order to represent and research the charge model of application layer in cloud computing clearly,the Petri net which introduces the cost and the profit to the transition is proposed.A concept and some theorems of cost-profit Petri net is put forward and used to describe the charge model of the application layer in cloud computing.Thus to the choice to the charge model of the provider of cloud computing,the reference model of analysis has built up.In addition,a specific example is given.