We reconstruct a proton exchange membrane fuel cell (PEMFC) catalyst layer (CL) and a non-woven carbon paper gas diffusion layer (GDL) by specially-designed stochastic methods. The reconstructed microstructures evidently distinguish all the participating components in the composite GDL/CL. Characterization analyses with respect to the reconstructed GDL/CL give important structural properties such as geometrical connectivity of an individual phase, pore size distribution, and volume-specific interfacial area. Self-developed Lattice Boltzmann (LB) models are established to calculate effective transport physical properties including effective thermal/electric conductivity and effective species diffusivity of the reconstructed GDL/CL, and permeability of the reconstructed GDL. Accordingly, we obtain tortuosity values for pore or solid phase in the reconstructed GDL/CL. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.