Shale is a complex porous medium. The migration mechanism within its different microstructural systems is crucial for the efficient recovery of shale gas. The kerogen microstructure influences the adsorption–desorption effect of the reservoir. This study accounts for the heterogeneity of shale and uses fractal dimension to characterize the fracture and inorganic matrix systems. It also establishes a kerogen fractal diffusion model by integrating fractal diffusion with fractal theory. Furthermore, this study analyzes the effect of evolution of micro structural parameters of kerogen on macro permeability, such as: (1) kerogen fractal dimension; (2) effective diffusion coefficient of kerogen; (3) maximum kerogen aperture. Numerical simulation shows that: The maximum pore size and porosity of kerogen in direct proportion to fractal dimension and effective diffusion coefficient. The fractal dimension and effective diffusion coefficient decrease gradually during shale gas extraction. The fractal effective diffusion has a significant impact on cumulative gas extraction.