The nanopores in shale reservoirs have large internal surface areas, and many gas molecules are adsorbed on the surface, forming an adsorption layer. The adsorption layer is mobile due to surface diffusion, which is driven by a chemical potential gradient. Traditional slip flow takes into account molecular collisions of free gas and porous surfaces but does not consider the influence of the motion of adsorption layers. In this study, free gas migration near wall surfaces is described using molecular dynamics and by considering collisions with the mobile adsorption layer. Further, a new slip coefficient model considering surface diffusion driven by a chemical potential gradient is proposed. The results show that the surface diffusion has a significant influence on gas slippage. The slip coefficient increases when considering the adsorption layer moving in small pores. When the pore pressure is less than 5 MPa and the pore radius is less than 5 nm, surface diffusion plays a dominant role in gas slippage. Based on the proposed slip coefficient, the influence of surface diffusion on the apparent porosity and transport capacity was analyzed. The results show that the apparent porosity first increases and then decreases as the pore pressure decreases; subsequently, it gradually increases as the pore radius decreases. The slip permeability and its contribution to transport capacity are greater than the viscous permeability in pores less than 10 nm, indicating that the slip effects have a significant influence on fluid flow in small pores.