It is of great significance to study shale apparent permeability under the action of multiple flow mechanisms and factors because shale reservoirs possess complex pore structures and flow mechanisms. In this study, the confinement effect was considered, with the thermodynamic properties of gas being modified, and the law relating to the conservation of energy adopted to characterize bulk gas transport velocity. On this basis, the dynamic change of pore size was assessed, from which shale apparent permeability model was derived. The new model was verified by three steps: experimental and molecular simulation results of rarefied gas transport, shale laboratory data, and comparison with different models. The results revealed that, under the conditions of low pressure and small pore size, the microscale effects became obvious, which significantly improved gas permeability. Through comparisons, the effects of surface diffusion and matrix shrinkage, including the real gas effect, were obvious in the smaller pore sizes; nevertheless, the stress sensitivity effect was stronger in larger pore sizes. In addition, shale apparent permeability and pore size decreased with an increase in permeability material constant and increased with increasing porosity material constant, including internal swelling coefficient. The permeability material constant had the greatest effect on gas transport behavior in nanopores, followed by the porosity material constant; however, the internal swelling coefficient had the least effect. The results of this paper will be important for the prediction and numerical simulation of apparent permeability relating to shale reservoirs.