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Proton exchange membrane fuel cell (PEMFC) is widely regarded as the most promising candidate for the next generation power source of automobile, after the pure battery electric vehicle. In this study, the gas and liquid two-phase flow in channels and porous electrodes inside PEMFC coupled with electrochemical reaction is simulated in detail, in which the anisotropic gas diffusion layer (GDL) is also considered. In the simulation, the inlet reactant gas molar concentration is calculated based on the real inlet pressure, which is more practical than specifying a constant value in previous simulation. Meanwhile, the effect of electro-osmotic drag on membrane water content distribution is treated to be a convection term in the conservation equation, instead of a source term as usually used.