In the present study, we develop a two-phase, non-isothermal, three-dimensional model of PEMFC to simulate cell performance. The model is based on five conservation equations(mass, momentum, species, energy, charge) and the liquid water equation. In this model, it can describe the phase change of water by evaporation/condensation effect, and the water transportation from electro-osmotic drag effect. In the practical application of the PEM fuel cell, liquid water would exist at high current density, it reduce the diffusivity of the gas phase species. If the pores in a porous media are occupied by liquid water, the gas phase species can not reach the catalyst layer. In past studies, effective medium theory is commonly adopted to calculated effective diffusivity. Here, we modify the effective diffusivity to simulate the area blockage effect due to the liquid water effect, validated by the network model proposed by Nam and Kaviany[7], the effective medium theory always overestimates the cell performance at high current density. However in our model the novel formulation can predict the cell performance precise validated by experiment data. Finally, the "one-dimensional two phase and non-isothermal" model of MEA with MPL has been adopted. The micro porous layer will reduce the liquid water at gas diffusion media and also improve the cell performance.