Abstract There are abundant nanopores in the organic matter of shales. Gas flow in nano-pores leads to micro-scale effect that can't be described by flowing law of macro fluid. The Lattice Boltzmann Method was applied to simulate gas flow in the nano-channels of organic matter and the effect of slippage, diffusion and adsorption/desorption were considered. The simulation result shows that the compressibility effect of gas leads to the nonlinear pressure distribution along the channels, and the larger the pressure difference, the more serious the nonlinear distribution. To some extent, the enhancement of rarefaction effect weakens nonlinear degree caused by the compressibility effect. With increasing Knudsen number and the pressure differential on the two ends, the slip velocity on the boundary increases, and the velocity vertical to the channel is not zero, increasing the exchange of kinetic energy between gas molecules in channels and molecules at boundary. Slippage effect and adsorption/desorption effect have a significant contribution to the gas mass flow in nano-channels of organic matter.