Traditional dual-porosity models average gas pressure within the matrix, failing to account for the uneven gas pressure distribution and the resulting inhomogeneous deformation in the shale skeleton. To this end, we propose a modified dual-porosity model. In the new approach, the gas pressure profile within the matrix is determined using the gas diffusion equation, and the induced deformation is expressed analytically and then integrated into the permeability model to establish a coupling process. The experimental data for both adsorption and non-adsorptive gases are accurately replicated to verify the proposed model. Subsequently, the effects of shale matrix properties -diffusion and geometry characteristics - on permeability evolution are addressed. Both global and local deformations together affect the permeability changes of adsorption gas. In contrast, for non-adsorptive gas, permeability is primarily driven by local deformation, influenced by the competition between inward and outward swelling. As a result, the recovery phase, primarily determined by the swelling transition, is more easily attained for non-adsorptive gas. The decreasing and recovering stages are more pronounced near the injection boundary, while areas farther from the injection boundary continue to experience reduced permeability. An increased diffusion coefficient leads to a reduced equilibrium time and a more pronounced global effect, resulting in an earlier rise in permeability evolution. A larger critical ratio produces a stronger local effect along with a notable decrease in permeability. Additionally, smaller matrix blocks exhibit a shorter equilibrium time and a greater global effect, resulting in a more significant reduction in permeability and a subsequent rebound. This work can provide an accurate method for evaluating the permeability variation in the laboratory and further the gas depletion characteristics at the field scale.