In automotive Polymer Electrolyte Fuel Cell (PEFC) system, dry gas purge operation is needed at shutdown condition in order to remove the liquid water in gas diffusion layer (GDL) and to reduce the oxygen diffusion inhibition by liquid water in GDL. However, exceed drying operation leads to degradation of electrolyte membrane because of little water content. Therefore, drying process has to be optimized. In this study, various GDL structure with unique fiber orientation were simulated by numerical analysis, and the real GDL structure was reconstructed by X-ray CT image of carbon paper GDL. Next, our past two-phase network model was improved to include phase change effect. The multi-block two-phase network model based on an actual structure was developed by a direct 3D networking porous structure. As results, the evaporation interface area depended on the porous structure of GDL, and the overall evaporation rate of homogeneous GDL which has uniform structure was 1.5 time higher than that of heterogeneous GDL because of the difference of this interface area. In addition, in the case of rib and channel, liquid water under channel evaporated faster than that under Rib. It is very important to control the drying operation in order to prevent the excess membrane drying.