Higher power density is needed to make compact and cost-competitive polymer electrolyte membrane (PEM) fuel cell stack. Key challenge to design a high power density fuel cell is to reduce oxygen transport loss caused by liquid water inside gas diffusion layer (GDL). However, liquid water transport through catalyst layer to GDL, GDL to channel under operating condition is not fully understood because of GDL’s small pore sizes (0.1~100μm), complex structure (formed of 2 porous layers: substrate layer and micro porous layer) and transport phenomena. To elucidate relationship between cell performance and water distribution, liquid water visualization technique by Synchrotron X-ray (SPring-8) and a Computational Fluid Dynamics (CFD) based simulation were developed and analyzed using design of experiments (DOE). Numerical model with DOE was used to calculate GDL parameters (thermal resistance, diffusion coefficient and capillarity pressure) impact on water distribution and cell performance. The calculation results show that thermal conductivity have most impact on water distribution and water distribution under channel have most impact on cell performance at relatively high humidity and current density condition. To validate the calculation results, water distribution and current density of two kinds of GDL with different thermal resistance were observed using SPring-8. Cross sectional 2D views (time resolution:1.5s/flame space resolution:1.3μm/pixel) of operating fuel cell was successfully achieved. Cathode GDL with higher thermal resistance substrate and lower thermal resistance micro porous layer was filled with less liquid water under the channel. Water distributions and performances showed same trend between numerical model and visualized cell. Combining developed techniques, relationship between GDL parameters, water distribution and fuel cell performance were clarified.