In recent years, e-commerce system has become an indispensable part of people’s daily life. In this way, the problems in the operation and management of this system are gradually exposed. This paper applies evolutionary game theory to explore evolution and optimal strategy for the harmonious development of the three parts, consumers, expressmen and e-commerce platforms. An three-part evolutionary game mode is presented among them, which takes into account the financial penalties and the degree of supervision of e-commerce platform. Then, the evolutionary stability strategies are analyzed by the differential equation theory and Liapunov stability analysis. Furthermore, numerical simulation is used to analyze the influence of several factors on evolution results. Research concludes optimal evolutionary strategy for this system: the consumer chooses the non-complaint strategy, the expressman chooses seriousness strategy, and the e-commerce platform chooses strict-management strategy. This paper can provide methods and strategies for the long-term stable evolution of similar system like e-commerce system.