Microporous layer (MPL), as a critical constituent of the proton exchange membrane fuel cell (PEMFC), plays a key role in mass, heat, electron, and species transport. The cracks formed during the deposition process on the surface of MPL change the overall transport capacity and effect the output performance of PEMFC. In this study, a 2D Lattice Boltzmann Method (LBM) pseudopotential multicomponent model is used to investigate the effects of perforated cracks in MPL on distribution, pressure drop and flow state of liquid water. The simulation results show that Capillary number (Ca) of liquid water in perforated cracks is around two orders of magnitude higher than Ca in twisty pores. Perforated cracks in MPL can not only reduce capillary resistance but also convert liquid water from capillary fingering to viscous fingering essentially, thus enhancing the permeability of liquid water in the through-plane direction while reducing the invasion in the in-plane direction. In consideration of gas-liquid transportation and other structural characteristics of GDL, the proper interval between perforated cracks with width of 10 μm is 3–6 crack diameters. This study provides reference for the design of functional pore structure MPL and conducts guidance for further research on PEMFC.