PEMFC (proton exchange membrane fuel cell) 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 electro-chemical reaction are simulated in detail, in which the anisotropic GDL (gas diffusion layer) 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 distribution is treated to be a convection term in the conservation equation, instead of source term as usually used. It can be concluded in the simulation that increasing the cathode stoichiometry ratio can facilitate the liquid water removal process in cathode channel and therefore decrease the liquid saturation in porous electrodes. It is also found that the higher the contact angle at the interface of BP (bipolar plate) and channel, the less the liquid water in channel and the higher the performance of PEMFC. Moreover, increasing the contact angle of cathode GDL will increase the liquid saturation in porous electrodes and the water in membrane and CL (catalyst layer) but decrease the liquid amount in cathode channel. Meanwhile, decreasing the cathode humidity appropriately is helpful to improve the performance of PEMFC because of the increase of oxygen concentration when the anode humidity is sufficient (e.g. 1.0). However, if not, it will decrease with the decrement of cathode humidity.