With the development of third-party payment in China, to some extend, it alleviates the problem of e-commerce and helps the development of e-commerce as well. However, it also brings some new issues, especially about government supervision. In this paper, the necessity of government supervision from three aspects is discussed because of the financial risks caused by the third-party payment. Furthermore, the theoretical government supervision model is proposed to demonstrate the best regulatory point for policy formulation based on cost-utility analysis.