A 3D lattice Boltzmann model is developed to simulate the pore-scale two-phase flow in the porous transport layer (PTL). The PTL, composed of the gas diffusion layer (GDL) and the micro porous layer (MPL), is stochastically reconstructed and validated by comparing the pore size distribution (PSD) with experimental data. This work focuses on the effect of MPL on liquid water transport in terms of hydrophobicity, PSD and structure. It is found that more hydrophobic material and smaller pore size apply higher local capillary force against the water transport. Water can only break through the crack-free MPL under an extremely high inlet pressure (about 400 kPa). Under the real operating conditions of a fuel cell, the PTL with single GDL suffers flooding with a low fraction of dry pore. With the presence of cracked MPL, the fraction of dry pore increases significantly since a large amount of water is constrained in the electrode and only the rest flows into the GDL through the cracks, which can keep the membrane hydrated and avoid flooding. Finally, a systematically designed PTL is proposed with uniformly distributed perforations, which can automatically balance the water content and further optimize the proton conductivity and reactant transport, simultaneously.