In order to avoid the “water flooding”, the excess water generating in PEM fuel cell should be drained timely. In this study, an experiment model was applied to analyze the path of water flow corresponding to the flow resistances based on the “flooding” between catalyst layer (CL) and gas diffusion layer (GDL). Narrow apertures in the largest pores of carbon paper gas diffusion layer are the primary resistance to liquid water penetration. After sufficient hydrostatic pressure is applied, water penetrates the limiting aperture and flows through the pore reaching the GDL surface. For the carbon paper GDL material, the pressure(~1 kPa)required for water to flow through the pores is much less than the pressure (~6 kPa) to penetrate the limiting aperture of the pores. Adding micro-porous layer (MPL) can obviously increase water penetrate resistance. The content of Teflon in the MPL has little effect on the water penetration pressure. It is helpful to promote the water management in fuel cell by setting pilot holes on the carbon paper GDL material.