Gas flow mechanisms and apparent permeability are important factors for predicating gas production in shale reservoirs. In this study, an apparent permeability model for describing gas multiple flow mechanisms in nanopores is developed and incorporated into the COMSOL solver. In addition, a dynamic permeability equation is proposed to analyze the effects of matrix shrinkage and stress sensitivity. The results indicate that pore size enlargement increases gas seepage capacity of a shale reservoir. Compared to conventional reservoirs, the ratio of apparent permeability to Darcy permeability is higher by about 1–2 orders of magnitude in small pores (1–10 nm) and at low pressures (0–5 MPa) due to multiple flow mechanisms. Flow mechanisms mainly include surface diffusion, Knudsen diffusion, and skip flow. Its weight is affected by pore size, reservoir pressure, and temperature, especially pore size ranging from 1 nm to 5 nm and reservoir pressures below 5 MPa. The combined effects of matrix shrinkage and stress sensitivity induce nanopores closure. Therefore, permeability declines about 1 order of magnitude compare to initial apparent permeability. The results also show that permeability should be adjusted during gas production to ensure a better accuracy.