In this work, the influence rules of driving force, pore size, temperature and pressure on methane adsorption/desorption and flow in coal nanopores were investigated by the molecular dynamic method based on Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The investigation results show that the viscosity of methane gradually decreases with the increasing driving force, while its fluidity and flow velocity increase. Meanwhile, the absolute slip length decreases and the flow tends to the non-slip state. Generally, the adsorption density of methane is independent of the driving force, but greatly affected by the gas-solid action. Methane can be adsorbed on the pore wall of coal during its flowing. For a small pore diameter of coal, the methane is almost adsorbed without free status. With the increase of pore size, the influence of the wall van der Waals force on the free methane molecules is weakened, and thus the flow velocity of methane increases, leading to a large amount of free methane present in the pores. Consequently, the methane changes from the unimodal distribution to the symmetrical bi-modal distribution. For methane has lower viscosity and good fluidity in the large pores, the Hagen-Poiseuille equation is more suitable for the methane flow therein. As the temperature increases, the thermal motion of methane molecule is enhanced, the density of the adsorption layer decreases, and the methane flow rate increases. Thereby, the adsorbed methane on the pore wall of coal is desorbed into free methane, increasing the flow rate of methane. With the increase of pressure, the amount of methane in the pore increases, resulting in the strong collision among methane molecules, so that the flow resistance of methane increases to slow down its flowing. In this work, the methane adsorption/desorption and flow mechanism in coal nanopores was clarified from a microscopic perspective by establishing some more realistic models. Hence, the research results could provide a theoretical basis for promoting methane desorption and improving the efficiency of coalbed methane extraction in engineering applications.