Abstract This study aims to investigate how multiple parameters affect the two-phase flow in compressed gas diffusion layer (GDL). A stochastic model is adopted to reconstruct the GDL microstructures. Solid mechanics simulations on the reconstructed GDL microstructures are performed, based on the finite element method (FEM). Various pore morphologies and distributions of compressed GDLs are observed. Two-phase flow in GDL is simulated using a volume of fluid (VOF) model. Corner droplet (on the GDL surface) and water flow (emerging from GDL bottom) are considered. It is found that two-phase flow in the GDL is highly influenced by compression, fiber diameter, porosity, and GDL thickness. The results indicate that a larger fiber diameter or higher porosity contributes to the water transport due to larger average pore size. Furthermore, water removal from a thicker GDL is more difficult, whereas water transport in the lower part of a compressed thick GDL is easy.