The classical Darcy's law cannot effectively describe the microscopic flow rules of shale gas. In addition, conducting gas transport experiments in nanopores is difficult, and the correctness of the simulation results is not guaranteed. Studies on the flow and transmission of shale gas in microscopic nanopores can effectively guide the macroscopic numerical simulation of shale gas reservoirs, which is of great significance to the economical and efficient development of such reservoirs. In this work, the dimensionless relaxation time expression is modified, and the Peng-Robinson equation of state (P-R EOS) is introduced to the microscale gas flow lattice Boltzmann model. The influences of viscous flow, slippage effect, boundary Knudsen layer, adsorbed gas layer, and surface diffusion are considered, and the results are combined with the real isothermal adsorption experimental data of shale samples collected from the Longmaxi formation in Sichuan Basin. Finally, the contributions of various transport mechanisms to shale gas flow in nanopores and their influencing factors are studied. Results show that the gas velocity and mass flux (Q) obtained using the ideal gas EOS are higher than those obtained using P-R EOS under high pressure. When the effective pore diameter (H-e) is less than 5 nm, surface diffusion and its induced free flow are the main transport mechanisms of shale gas flow in nanopores. Viscous flow becomes the main transport mechanism when H-e exceeds 20 nm. H-e, pressure, and shale adsorption capacity significantly affect the contribution rate of each transport mechanism to the total Q of shale gas. By comparison, the influence of temperature on the Q of shale gas is relatively small and can be neglected under high pressure.