This study proposes a multiscale model combining molecular simulation and the lattice Boltzmann method (LBM) to explore gas flow behaviors with multiple transport mechanisms in nanoporous media of shale matrix. The gas adsorption characteristics in shale nanopores are first investigated by molecular simulations, which are then integrated and upscaled into the LBM model through a local adsorption density parameter. In order to adapt to high Knudsen number and nanoporous shale matrix, a multiple-relaxation-time pore-scale LBM model with a regularization procedure is developed. The combination of bounce-back and full diffusive boundary condition is adopted to take account of gas slippage and surface diffusion induced by gas adsorption. Molecular simulation results at the atomic scale show that gas adsorption behaviors are greatly affected by the pressure and pore size of the shale organic nanopore. At the pore scale, the gas transport behaviors with multiple transport mechanisms in nanoporous shale matrix are explored by the developed multiscale model. Simulation results indicate that pressure exhibits more significant influences on the transport behaviors of shale gas than temperature does. Compared with porosity, the average pore size of nanoporous shale matrix plays a more significant role in determining the apparent permeability of gas transport. The roles of the gas adsorption layer and surface diffusion in shale gas transport are discussed. It is observed that under low pressure, the gas adsorption layer has a positive influence on gas transport in shale matrix due to the strong surface diffusion effect. The nanoporous structure with the anisotropy characteristic parallel to the flow direction can enhance gas transport in shale matrix. The obtained results may provide underlying and comprehensive understanding of gas flow behaviors considering multiple transport mechanisms in shale matrix. Also, the proposed multiscale model can be considered as a powerful tool to invesigate the multiscale and multiphysical flow behaviors in porous media.