Quantitative characterization of shale gas flow in fractured shale is a key problem in shale gas extraction. In this study, 3D multi-scale structures in fractured shale were reconstructed, firstly, by X-ray micro-computerized tomography (CT), high-resolution scanning electron microscope (SEM), and fractal function. Then, a REV (representative elementary volume)-scale lattice Boltzmann (LB) model, considering Klinkenberg’s effect and gas absorption, was built, and the effects of fracture complexity and gas pressure on shale gas flow and shale permeability were analyzed and studied quantitatively. The simulation results indicate that the gas flow behaviors in the fractured shale are related strongly to fracture morphology and gas pressure. The decreased fracture fractal dimension or increased complexity of the fracture network leads to increase in permeability of the fractured shale. The gas velocity in the shale matrix decreases with increasing fracture roughness. Increased fracture network connectivity contributes to the formation of local high-intensity velocity fields and the improvement of gas flow in the shale matrix. The gas rarefaction effect has a significant influence on gas flow in the fractured shale, and permeability of the fractured shale must be regarded as a dynamic shale reservoir parameter. The gas flow behavior in the fractured shale is more sensitive at low-pressure condition whereas the gas rarefaction effect is more sensitive to the fractured shale with highly rough fracture or low fracture connectivity.