In this paper, a three-dimensional, complex seepage model of a proton exchange membrane fuel cell (PEMFC) is studied, the corresponding finite element method and numerical simulation are given as well, where species transport, fluid flow, charge transport, heat transfer and electrochemical reaction in the PEMFC are simultaneously addressed. The domain to be studied includes porous gas diffusion layers, catalyst layers, gas channels, bipolar plates, and membrane. The fluid transportation phenomena arising in the whole fuel cell are described by the referred model, different physical parameters and source terms are reflected in different areas. The chemical components, flow characteristics and distributions of temperature in the 3-D space are obtained by resolving the seepage control equation system coupled with electrochemical equations. The induced methods and results can guide the optimal design of PEMFC.