Proton exchange membrane fuel cells have been promoted due to improved breakthrough and increased commercialization. The assembly pressure put on a single cell and a fuel cell stack has important influence on the geometric deformation of the gas diffusion layers (GDLs) resulting in a change in porosity, permeability, and the resistance for heat and charge transfer in proton exchange membrane fuel cells. In this paper, both the finite element method and the finite volume method are used, respectively, to predict the GDL deformation and associated effects on the geometric parameters, porosity, mass transport property, and the cell performance. It is found that based on the isotropic Young's modulus and the finite element method, the porosity and thickness under a certain assembly pressure are non-homogeneous across the fuel cell in the in-plane direction. The variations of the porosity change and compression ratio in the cross-section plane are localized by three zones, that is, a linear porosity zone, a constant porosity zone, and a nonlinear porosity zone. The results showed that the GDL porosity and compression ratios maintain linear and nonlinear changes in the zone above the shoulders and the zone under the channel but close to the shoulder, respectively. However, a constant value is kept above the middle of the channel. The obtained non-homogeneous porosity distribution is applied together with the deformed GDL for further computational fluid dynamics analysis, in which the finite volume method is implemented. The computational fluid dynamic results reveal that a higher assembly pressure decreases the porosity, GDL thickness, gas flow channel cross-sectional areas, oxygen diffusion coefficient, oxygen concentration, and cell performance. The maximum oxygen mole fraction occurs where the maximum porosity exists. A sufficient GDL thickness is required to ensure transfer of fresh gas to the reaction sites far away from the channel. However, the reduction of porosity is a dominating factor that decreases the cell performance compared with the decreased gas channel flow area and GDL thickness in the assembly condition. Therefore, the assembly pressure should be balanced to consider both the cell performance and gas sealing security. Copyright (c) 2017 John Wiley & Sons, Ltd.