It is very important to understand the transport phenomena under various operating and structural conditions to achieve the high performance of Polymer Electrolyte Fuel Cell (PEFC). In this study, the effect of liquid water removal inside flow channel on the performance of a large-sized cell was investigated. To calculate the performance of a cell or stack, we developed a simulation tool with macroscopic models of MEA characteristics such as electrochemical kinetics, catalyst utilization, limiting current density, and two-phase transport inside the gas diffusion layer (GDL) and the flow channel. At first, we investigated the effect of wall contact angle and cross-section of flow channel on the liquid water removal by the Moving Particle Semi-implicit method and calculated the velocity ratio (liquid water velocity for gas velocity) inside the flow channel including the effect of mesoscopic structure of GDL. Applying this correlation to the two-phase model of the macroscopic PEFC simulation, we confirmed that the performance in the case of hydrophilic and shallow-shaped channel is much better in other case under low utilization operation.