ABSTRACT Gas diffusion layer (GDL) is an important pathway for water transport in the proton exchange membrane fuel cell. The presence of excessive liquid water in the cathode GDL will cause “water flooding” and block the reactant transport path to catalyst sites. Therefore, it’s critical to understand water transfer mechanism in GDL and propose novel strategy to improve water management. In this study, the effect of GDL with different perforation holes on liquid water transport behavior are investigated by volume of fluid method. The simulation model is validated by comparing with the reported data. The results show that the GDL with perforation holes will accelerate the liquid water breakthrough. Specially, the GDL with cylindrical perforation achieves the lowest breakthrough pressure, and most excellent water drainage capacity under various pressure drops. The gradient hydrophobic distribution in GDL will improve the water breakthrough path and drainage capacity. However, gradient hydrophobic treatment in GDL with conical perforations will result more water leakage along the though-plane direction. The simulation results will provide significant guidance for designing high performance GDL and improving the water management in proton exchange membrane fuel cell.