In this study, a three-dimensional, non-isothermal, two-phase flow mathematical model is developed and applied to investigate the effect of the GDL deformation on transport phenomena and performance of proton exchange membrane (PEM) fuel cells with interdigitated flow fields. The thickness and porosity of the GDL is decreased after compression, and the corresponding transport parameters (permeability, mass diffusivity, thermal conductivity and electrical conductivity) are affected significantly. The alterations in geometry and transport parameters of the GDL are considered in the mathematical model. The oxygen concentration, temperature, liquid water saturation and volumetric current density distributions of PEM fuel cells without compression are investigated and then compared to the PEM fuel cells with various assembly forces. The numerical results show that the cell performance is considerably improved with increasing assembly forces. However, the pressure drops in the gas flow channels are also substantially increased. It is concluded that the assembly force should be as small as possible to decrease the parasitic losses with consideration of gas sealing concern. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.