Traditional theoretical models used to predict shale permeability generally ignore the influence of the effective stress and gas sorption-induced strain on the gas transport process. Consequently, the predicted permeability may deviate from the experimental results, wherein the coupling effect of the fluid and solid is involved. To improve the accuracy of the permeability model for shale stones, a hydraulic diameter-based generic permeability model was proposed that couples the effective stress, gas sorption, and flow-regime effects. Three special degenerate case models, based on the generic model, were validated using three corresponding experimental conditions. Sensitivity studies have demonstrated that the flow-regime effect is sensitive to the size of the equivalent hydraulic diameter, whereas the poroelastic effect is sensitive to the initial porosity and compressibility factor of the shale bulk. The two effects cannot be decoupled from shale permeability during the experimental process. The contribution of the adsorption effects to permeability, as reflected by the Langmuir pressure constant of the matrix, is greater in the high-pressure region, where pore elasticity dominates. The contribution of the adsorption effects to permeability, as reflected by the Knudsen number, is weaker in the low-pressure region, where the flow regime dominates. In addition, the contribution of the adsorption effect varies much more in the poroelasticity deformation than in the fluid dynamics.