In order to improve the output performance of PEFC, it is important to investigate the two-phase condition in gas diffusion layer (GDL). In this study, the simulated GDL structure was developed by numerical analysis including the random orientation of carbon fibers and binders. And detailed structural estimation was carried out. As structural properties, pore size distribution, electrical resistivity and tortuosity were calculated, and these values almost agreed with actual measurement values. Furthermore, our past two-phase network model was improved, and the model based on an actual structure was developed by a direct 3D networking porous structure. And the influence of GDL structure on the two-phase condition with accumulated water was evaluated, and effective diffusion coefficient of oxygen in GDL with liquid water was calculated.