We present the analysis of gas transport in micro porous layers of polymer electrolyte fuel cells based on the three-dimensional structure data obtained from X-ray nano computed tomography (CT). The characteristic pore size is comparable to the mean free path of gas molecules. The polygonal surface representation of the porous structure is constructed from the volumetric CT image using the marching tetrahedrons algorithm. The diffusion fluxes of gas molecules through the porous layer are evaluated by the direct simulation Monte Carlo method, which can reproduce the transition between the Knudsen and molecular diffusion regimes. Our numerical simulation well reproduces the experimentally observed pressure dependence of the diffusion resistance. The effect of porous media morphology on gas transport is examined by an analysis of the trajectories of transmitted molecules through the porous layer.