An accurate understanding of gas seepage mechanisms in shale reservoirs would have a positive impact on promoting shale gas development. Shale is a complex dual-porosity medium composed of a microfracture network and capillary network. However, most shale dual-porosity permeability models have usually ignored the influence of key mechanisms, such as effective stress and gas adsorption. In addition, the depiction and analysis of the Knudsen number has not been fully discussed in previous studies. In this study, the inner relationship between intrinsic permeability and porosity has been taken to be a bridge, with the fracture width including the pore radius being quantified, leading to a modification of the Knudsen number in the microfracture network and capillary network. Based on the modified Knudsen number, a dual-porosity permeability model has been developed for typical shale reservoirs that considered real gas effect, flow regimes, effective stress, and gas adsorption. The reliability of the new model has been validated by published experimental data under different conditions and through comparisons with the existing theoretical models. Finally, the evolution law relating to gas apparent permeability and the Knudsen number in the microfracture network and capillary network has been discussed, and the effects of different factors concerning apparent permeability and the Knudsen number have been quantified. Based on the results, the relationships between the coupled effects relating to the rock deformation field, the microfracture network seepage field, the capillary network seepage field, and the Knudsen number have been proposed. Moreover, the mechanisms relating to the internal swelling coefficient and gas rarefaction coefficient, including different pore network occupancies on total gas transport capacity, have been presented. The research results will provide a basis for the accurate numerical simulation for shale gas and will be of great significance to the economic development of shale gas in the future.