Selection of flow channel in the separation plate of PEMFC is very important parameter to improve its performance and reduce parasite loss. Flow patterns in the channel have great influence on the transport of hydrogen and air and removal of water generated from electrochemical reaction in diffusion layer. In this study. fluid flow in flow channel with parallel and interdigitated patterns are simulated three dimensionally on full flow domain including anode and cathode channel together. The numerical results show that the fuel cell with interdigitated flow channel represents better performance than that with parallel flow channel due to its strong convective transport across the gas diffusion layer. But the pressure drop in parallel flow channel is much more than that in interdigitated flow channel. And effects of temperature and stoichiometric number on performance can be calculated and analyzed as well. Nomenclature.