Abundant nanopores were observed in gas shales using field emission scanning electron microscopy. The Navier-Stokes equation based on the continuum assumption breaks down at the nanometer scale. The transport mechanisms of gas in nanopores of shales have been simulated using the Lattice Boltzmann Method. The simulation result shows that the microscale phenomenon of gas in nanopores of shales leads to bigger average flow rates than that from the classic Poiseuille equation. The rarefaction effect is very remarkable, and the slip velocity on the wall boundary is not equal to zero. The smaller the pore diameter is, the larger the slip velocity is, so much so that the slip velocity becomes bigger than gas velocity in the nanopores, and the parabola flow velocity profile transforms from parabola to plunger. The “double skip effect” which results from the rebounding gas molecules with kinetic energy entering into the nanopores enhances the flow of gas in the whole nanopores, which bring about increased actual permeability, and the permeability of nanopores is bigger than that from liquid permeability. In addition, the “double skip effect” leads to nonlinear deviation from the classic Klinkenberg slip theory, especially in low flow pressure and smaller pore diameter.