Computational fluid dynamics (CFD) simulations were conducted to study the liquid water transport behaviors in flow channels of polymer electrolyte membrane fuel cells (PEMFCs). The effects of geometries and surface properties of flow channels on the liquid water exhaust capabilities were quantitatively analyzed based on the exhaust time and stagnant volume data obtained by the CFD simulations. Two different liquid morphologies were found to develop during the two-phase (water/air) transport in flow channels: liquid film morphology for hydrophobic channels and droplet morphology for hydrophilic channels. It was also observed that hydrophobic channels exhausted liquid water much faster than hydrophilic channels, but the stagnant liquid volume in corners of hydrophobic channels was larger than that of hydrophilic channels. The exhaust capability results determined by the quantitative analysis were explained by referring to the different morphologies of liquid water in flow channels.