A better understanding on gas flow in nanopores will advance the knowledge of gas accumulation and preservation in shale as well as development of shale gas exploitation. A modified LB model for nanoscale shale gas flow under basin condition was established, by considering the volume reduction effects of the adsorbed layer and introducing the equation of state of methane gas. Methane flow simulations in slit pores under different conditions are conducted to investigate the effects of temperature, pressure, pore size, and buried depth on nanoscale shale gas flow. It is revealed that the apparent permeability (AP) increases with the decrease of pressure and pore size but increases with temperature, while the intrinsic permeability (IP) remains the same with them. The difference between the AP and the IP increases with temperature but decreases with pressure and pore width. For a certain pore width, the AP is always larger than the IP and decreases with buried depth, while IP does not change. It is deduced that with the increase of buried depth, the migration of shale gas in nanopores is suppressed, and it gets close to the liquid flow at a very high buried depth. Thereafter, the cut off pore throat (COPT) of methane flow for a shale with different pore size distributions under different buried depths was predicted. The calculated COPTs of methane flow increase with buried depths or/and the pressure coefficients and are always smaller than the COPTs of intrinsic ones (approximately equal to liquid flow). As buried depth or pressure coefficient a p increase, the shale gas migration is suppressed, and the shale gas flow nature of shale gas gets close to the traditional macroscopic seepage when the buried depth is very deep. For examples of shale rocks with different pore size distributions (PSDs) buried at 4 km depth with a pressure coefficient of 1.0, the COPTs for methane flow are 4.50, 8.57, 12.73, and 21.07 nm, respectively. It means that nanoscale pores (even small than 5 nm) make important contributions to the shale gas migratability in reservoirs, and for shale rocks with similar PSD characteristic, the COPT decreases with average pore size.