A fundamental understanding of polymer electrolyte membrane (PEM) fuel cell material degradation and performance variation under various operating conditions requires numerical models that accurately describe coupled electrochemical, charge, mass, and heat transport, as well as the structural response (deformation) of fuel cells. An integrated model representing the charge and mass transport, electrochemical reactions, and structural response was attempted in this work based on a unified finite element modeling technique for analyzing these coupled phenomena. The model accounted for the inhomogeneous gas transport properties of gas diffusion layer (GDL) and the electrical contact resistance as a function of stress distribution in the compressed GDL, as well as the swelling of ionomer membranes due to water absorption. For the mechanical modeling of the ionomer membranes, a micromechanism-inspired viscoelastic model with hygrothermal expansion was used. The analysis showed cell compression effects on both the fuel cell performance and the mechanical stress distribution in membranes under realistic fuel cell operation conditions. The results showed dramatic changes in gas transport properties and current density profiles with respect to the degree of cell compression and the stress distribution in the membrane altered by the operating conditions such as relative humidity and current density.