With the development of Internet, especially communication technology, smart phones and Web2.0, the increasing popularity of mobile E-commerce appears. However, the natures of multiple network interfaces in smart mobile devices and design flaws of mobile payment protocols and mechanisms make security issues become more serious. The mobile payment system network architecture which comprises contactless layer, control layer, network layer, and application layer is analyzed. And the basic process of mobile payment is put forward. And then, the existing network system security issues of each layer are analyzed, including contactless layer security, control layer security, network layer security, and application layer security. The mobile payment protocols and their improvements are analyzed and summarized. The security assessment methods are also analyzed, compared and summarized. Moreover, A new secure mobile payment system network architecture is given. Finally, the summary of the existing security research is processed,And the future research direction is put forward.