Gas flows in the forms of multiple transport mechanisms in shale nanoporous media with complex pore structure and different pore types. Laboratory pressure pulse decay technique is often applied to measure gas permeability but the current gas permeability interpretation model is mostly based on the homogeneous macro scale model while the influence of pore structure on real gas transport is neglected. In this study, a novel pore structure based real gas transport model is proposed to determine gas permeability in nanoporous shale combining laboratory pressure pulse decay technique with pore network simulation. The laboratory pressure pulse decay process is simulated in a virtual system based on the similarity principle which contains upstream vessel, downstream vessel, and core sample. The core sample is constructed by a series of connected pore networks and the sizes of pores and throats in each location of the pore network are randomly assigned according to laboratory measured pore size distribution. Gas transport mechanisms inside the core sample consider viscous flow, Knudsen diffusion, surface diffusion and real gas effect. At each time step, the upstream vessel pressure decreases and the downstream vessel pressure increases until the upstream vessel pressure and downstream vessel pressure become equal. The simulated pressure drop versus time curve is obtained and is applied to fit the laboratory measured pressure drop data by repeating core sample construction and pressure pulse decay process. The proposed model is applied to measure gas permeability of Sichuan basin, Longmaxi formation shale core sample. The results indicate that the predicted value based on the proposed model matches well with the experimental measured pressure drop data. The proposed model is used to study the influences of test gas type and pore size on gas permeability. When the average organic pore radius is less than 20 nm, helium tested permeability overestimates at least 40% of the methane permeability. (C) 2018 Elsevier Ltd. All rights reserved.