Natural gas (methane is the primary constituent) adsorbed on nanoporous materials is a promising alternative to compressed natural gas as a cleaning fuel. To understand the transport of methane confined in a nanoscale pore is useful for developing and optimizing some related industry processes. Equilibrium molecular simulation were carried out to study the transport behaviors of methane confined in two types silica pores, a cristobalite silica pore and an amorphous silica pore. Many factors, such as temperatures, densities of methane and surface structures of pore, which could affect the transport of methane, were examined in simulations. Simulations calculated the diffusion coefficients of methane at different densities and temperatures. The detailed microscopic structures of pores have a great correlation with the diffusion behaviors of methane. The diffusion coefficients of methane increased with increasing temperature, but decreased with the increase of density.