In order to commercially develop shale gas reservoirs, it is necessary to understand the gas transport mechanisms in shale matrix and how matrix permeability evolves during reservoir depletion. In this work, improved apparent permeability models to describe gas transport through microstructures (i.e. micropores and microfractures) in organic matter (OM) and inorganic matter (iOM) of shale matrix are proposed. The models are able to consider the combined effects of poromechanics, non-Darcy flow, gas sorption and fractal dimension of microstructures on gas flow behavior. The obtained results indicate that microfracture aperture declines by a larger margin than micropore diameter when reservoir depletes. A greater microstructure size fractal dimension and maximum microstructure size lead to a larger apparent permeability, while a greater tortuosity fractal dimension leads to a smaller apparent permeability. In shale matrix, the apparent permeability of inorganic microstructures is much larger than that of organic microstructures. In OM or iOM, when micropores and microfractures have the same cross-section area, the apparent permeability of micropores is larger than that of microfractures. Furthermore, for microstructures in OM, the contribution of different flow regimes to total gas flow varies with pore pressure and microstructure size. For microstructures in iOM, the contribution of slip flow dominates the gas transport. The obtained results provide new insights for understanding gas transport behavior in shale reservoirs from a microscopic perspective.