Accurate capillary pressure-liquid water saturation relationship (p(c)-s) plays a key role in predicting the performance of proton exchange membrane (PEM) fuel cells and the two-phase flow characteristics in gas diffusion layer (GDL). In this work, a validated Leverett function (K-function) based on the experimental p(c)-s data for SGL24 and SGL10 series carbon paper GDL materials is incorporated into a three-dimensional and two-phase PEM fuel cell model to investigate the effects of gas diffusion layer properties on the cell performance. Special emphasis is put on Polytetrafluoroethylene (PTFE) loading (5-20 wt%) in the GDL, compression pressure (1-4 MPa) and micro-porous layer (MPL). The results show that the cell exhibits better performance when a higher PTFE loading of 20% and a lower compression pressure of 1 MPa are adopted. However, liquid water is hard to drain from the GDL with the 5 wt% PTFE loading due to the low hydrophobicity, especially under the ribs; for the high compression pressure of 4 MPa, small effective porosity caused by the pressure becomes the major resistance of water drainage. The existence of MPL is also very helpful to reduce the water saturation in the GDL. (C) 2016 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.