Numerical simulations using the lattice Boltzmann method (LBM) are developed to elucidate the dynamic behavior of condensed water and gas flow in a polymer electrolyte membrane (PEM) fuel cell. Here, the calculation process of the LBM simulation is improved to extend the simulation to a porous medium like a gas diffusion layer (GDL), and a stable and reliable simulation of two-phase flow with large density differences in the porous medium is established. It is shown that dynamic capillary fingering can be simulated at low migration speeds of liquid water in a modified GDL, and the LBM simulation reported here, which considers the actual physical properties of the system, has significant advantages in evaluating phenomena affected by the interaction between liquid water and air flows. Two-phase flows with the interaction of the phases in the two-dimensional simulations are demonstrated. The simulation of water behavior in a gas flow channel with air flow and a simplified GDL shows that the wettability of the channel has a strong effect on the two-phase flow. The simulation of the porous separator also indicates the possibility of controlling two-phase distribution for better oxygen supply to the catalyst layer by gradient wettability design of the porous separator.