The nanopore structure usually exhibit complex geometry in the shale formation. The interactions between gas and pore structure in such heterogeneous property impacts the properties of shale gas transport in micro-scale. The precise description of this shale gas flow processes in detail is impossible if the micropore is not properly characterized. Thus, this study provides a simulation approach to model the complex geometry of nanopore structures in the shale formation. Based on SEM image segmentation of the shale matrix, the geometry of three compositions (nanopore, kerogen, and matrix) are explicitly simulated. Mass storage, transport mechanisms, and geomechanical properties are fully modeled in the micro-scale model. It demonstrates that the conventional dual porosity model fails to capture the storage and transport mechanisms in micro-scale by comparison with the micro-scale model. The simulation results reveal that stress-induced decrease of the diffusion coefficient is both time-dependent and space-dependent. The reduction of the diffusion coefficient can significantly cut down the adsorbed gas production in kerogen. It results in the low recovery rate of shale gas that a large proportion of adsorbed gas is unable to liberate. Moreover, the later stage of gas production is depended on the supply of adsorbed gas in kerogen.