In contrast to conventional gas-bearing rocks, gas shale has extremely low permeability due to its nanoscale pore networks. Organic matter which is dispersed in the shale matrix makes gas flow characteristics more complex. The traditional Darcy’s law is unable to estimate matrix permeability due to the particular flow mechanisms of shale gas. Transport mechanisms and influence factors are studied to describe gas transport in extremely tight shale. Then Lattice Boltzmann simulation is used to establish a way to estimate the matrix permeability numerically. The results show that net desorption, diffusion, and slip flow are very sensitive to the pore scale. Pore pressure also plays an important role in mass fluxes of gas. Temperature variations only cause small changes in mass fluxes. The Lattice Boltzmann method can be used to study the flow field in the micropore spaces and then provides numerical solutions even in complex pore structure models. Understanding the transport characteristics and establishing a way to estimate potential gas flow is very important to guide shale gas reserve estimation and recovery schemes.