Hydrogen crossover has an important effect on the performance and durability of the polymer electrolyte membrane fuel cell (PEMFC). Severe hydrogen crossover can accelerate the degradation of membrane and thus increase the possibility of explosion. In this study, a two-phase, two-dimensional, and multiphysics field coupling model considering hydrogen crossover in the membrane for PEMFC is developed. The model describes the distributions of reactant gases, current density, water content in membrane, and liquid water saturation in cathode electrodes of PEMFC with intrinsic hydrogen permeability, which is usually neglected in most PEMFC models. The conversion processes of water between gas phase, liquid phase, and dissolved water in PEMFC are simulated. The effects of changes in hydrogen permeability on PEMFC output performance and distributions of reactant gases and water saturation are analyzed. Results showed that hydrogen permeability has a marked effect on PEMFC operating under low current density conditions, especially on the open circuit voltage (OCV) with the increase of hydrogen permeability. On the contrary, the effect of hydrogen permeability on PEMFC at high current density is negligible within the variation range of hydrogen permeability in this study. The nonlinear relations of OCV with hydrogen diffusion rate are regressed.