Gas diffusion layer (GDL) in fuel cell plays an important role of passage for reactant transport and water removal between the bipolar plate and the electrode. In the present work, effective transport physical properties of gas diffusion layer in proton exchange membrane fuel cells (PEMFC) are deduced using lattice Boltzmann simulation, which is applicable for both GDL substrate with a pore size of 10~100 micrometer and MPL with 10~100 nanometer pore size. We also use GDL microstructure scanned using high resolution X-ray computed tomography and compressed under realistic levels with virtual material design tool. Liquid water saturation in the GDL is considered in the simulation because the blockage of pores by water has a strong influence on its effective gas transport properties. The deduced properties can be applied to fuel cell performance program and its influence on cell performance be measured.