PEM fuel cell is the most promising application as an automotive power. Proton transfer in PEM is one of important factors to understand the performance of PEM fuel cell. In this paper, the proton transfer mechanisms are analyzed by the molecular simulation based on the basic principle of molecular dynamics. Effects of water content in the proton exchange membrane and cell temperature on the proton transfer in the membrane are studied by the radial distribution function (RDF). Results show that proton transfers in the Nafion polymer by water bridges between two sulfonic groups of adjacent side chains. There are more water bridges supporting proton transfer with the increase of water content in membrane. The increase of cell temperature speeds up the form and break of O-H bond, which promotes the proton transfer. The research results are very helpful to understanding the proton transfer mechanism in proton exchange membrane and promoting the applications of PEM fuel cell.