As a kind of clean energy, proton exchange membrane fuel cell (PEMFCs) are expected to become power source of vehicles. Microporous layer (MPL) enhances the output performance of PEMFC by regulating water management. In this study, a 3D lattice Boltzmann method (LBM) pseudopotential multicomponent model is applied to investigate the effects of perforated cracks in MPL on liquid water distribution and flow regime of liquid water. The perforated cracks can not only reduce capillary resistance and water saturation but also promote liquid water from capillary fingering to viscous fingering essentially, which means enhancement of the permeability of liquid water in the through-plane direction and reduction of percolation in the in-plane direction. The liquid water in perforated cracks is insensitive to the wettability of MPL. This study can give guidance for the practical design and application of MPL with artificial pore structure.