Based on a coupled finite element method (FEM) and computational fluid dynamics (CFD) model, the structural deformation and performance of a proton exchange membrane fuel cell (PEMFC) under different membrane water contents are studied. The water absorption behavior of the membrane is investigated experimentally to obtain its expansion coefficient with water content, and the Young’s modulus of the membrane and catalyst (CL) are obtained through a tensile experiment. The simulation results show that the deformation of the membrane increases with water content, and membrane swelling under the channel is larger than that under the rib, forming a surface bump under the channel. The structural changes caused by the membrane water content have little effect on the performance of PEMFC in the low-current density range; while its influence is significant in the medium- and high-current density range. A medium membrane water content value of 12 achieves the best fuel cell performance due to the balance of membrane resistance and mass transport.