In order to achieve the data information secure transmission from the mobile terminal to the application server through the WAP gateway. By the analysis of the status of mobile E-commerce security, WPKI mobile E-commerce security system is designed based on the mobile E-commerce security system, WTLS state process model and WTLS news timing diagram are designed based on WPKI. With the help of double encryption mechanism, based on the theory of Petri net and WPKI mobile E-commerce security structure, security model of mobile E-commerce Petri net is established. By the use of CPNtools, simulation experiments are conducted. Conservation conditions, the feasibility and rationality index of the model are achieved by establishing incidence matrix. The experimental simulation analysis and output of experimental reports indicate that no deadlocks node exist at runtime, the business processes are properly designed, accessibility is meet and a good structure and coverage is contained which brings an effective solution to the security of data transmission of mobile Ecommerce.