It is important to investigate the two-phase condition in PEFC gas diffusion layer (GDL) to improve mass transfer rate. The structure of simulated GDL made of layered carbon fibers was produced by the numerical analysis in this study, and the structural properties of various simulated GDL were investigated, for example pore distribution, permeability and tortuosity. With these structures, the two-phase analysis model in GDL was developed with a 3-dimensional network model converted from simulated GDL directly, and the two-phase condition in GDL was calculated on various conditions of GDL structure and hydrophilicity. And the influences of multi-layer GDL structure were evaluated. As a result, it was confirmed that the liquid water distribution was affected by multi-layer structure and that optimizing the connection of porepore and changing the contact angle along the direction of water flowing out lead to decrease the amount of water and increase O2 diffusivity.