Abstract Although natural gas is widely produced from shale, the mechanisms of natural gas transport in shale matrices remain poorly understood due to the complex chemical compounds of the matrices and the nanoscale pore size distribution. Using molecular simulations, we investigate natural gas transport and storage in nano-pore networks. Carbon-based 3-D pore networks are generated from 2-D scanning electron microscopy (SEM) images of a shale rock using the Markov Chain Monte Carlo simulation method. We employ a grand canonical Monte Carlo (GCMC) simulation to calculate adsorption isotherms of natural gas in carbon-based 3-D pore networks, which can be fit by a Langmuir isotherm model. To investigate gas transport in the same structures, we insert an external driving force into non-equilibrium molecular dynamics (NEMD) simulations and find that Knudsen diffusion is the dominant transport mechanism in the pore networks. Although porosity and pore connectivity affect the natural gas diffusion in the pore networks, we typically observe a linear relationship between average molar flow rate through a cross-sectional area and the external driving force.