In a polymer electrolyte membrane fuel cell, the condensed water in the separator-channel prevents the supply of reactants to electrodes, which deteriorates the cell performance. The Lattice Boltzmann simulation has been conducted to understand the behavior of condensed water in the separator-channels. The scheme for the two-phase flow with large density difference was applied and the boundary condition for wettability at the corner inside the channel was examined. The present simulation demonstrates the effects of the cross-sectional shape, the wettability of channel and the volume of condensed water on the liquid water behavior. In the hydrophilic separator-channels, the liquid water spreads along the channel wall to form film and, in a specific condition, the water draws away from the gas diffusion layer, which suppresses the flooding. On the other hand, the liquid water forms sphere, covering larger area of the surface of gas diffusion layer in the hydrophobic separator-channels, but the drain performance of liquid water is superior.