Water management, particularly in the gas diffusion layers (GDL), plays an important role in the performance and reliability of the proton exchange membrane fuel cells (PEMFCs). In this study, a two-phase multiple-relaxation-time (MRT) lattice Boltzmann method (LBM) is employed to simulate water transport in a reconstructed GDL and the effect of perforation shapes is investigated. The revised pseudopotential multiphase model is adopted to realize high-density ratio, good thermodynamic consistency, adjustable surface tension and high contact angle. The transport characteristics are analyzed in both vertical and horizontal transport directions. The LBM simulation provides detailed results in mesoscale and indicates that the surface tension dominates the process of water transport in the perforated GDL, which exhibits unexpectedly similarities in the vertical and horizontal transport. Besides, it is found that the cone-like perforations perform better than cylinder-like perforations as little water clusters together in the bottom of the perforation. Finally, the optimized perforation with defined parameters is derived and discussed, providing guidelines for improving the GDL performance in engineering applications.