Organic-rich mudrock systems play an important role in the world's volatile petroleum industry. Due to their complex pore structures with a large portion of nano pores, the flow mechanics of gas flow in the pore space may involve nanoscale effects that could not be accounted for by classic Darcy's law. It is also very difficult to experimentally probe the transport properties of extremely low permeability rock samples. Digital rock physics (DRP) obtains a direct view of the internal structure of reservoir rock sample by digitized high resolution images to compute their properties, such as porosity and directional permeability, and hence to enable the studies of multi-scale flow mechanics in mudrocks. In this study, we present a parallel lattice Boltzmann method (PLBM) for studying nanoscale effects on a three dimensional (3D) tube flow, and then to simulate the flow process of the gas flow in real 3D pore geometry of two perpendicularly cored mudrock samples (S62H and S62V), combining with some image processing methods in DRP. The pore geometry is obtained by 3D digital image data based on ultra-high resolution X-ray computed tomography (XCT) imaging. The numerical advantages of lattice Boltzmann method (LBM) make it a powerful tool to simulate gas flow in such nano pores and estimate the absolute permeability. The new parallel implementation has been successfully performed on a powerful high performance computing cluster (HPCC) and validated with the analytical solution of a 3D tube flow model, which is taken as the elementary model for the pore networks. By simulating the nanoscale effects of rarefaction, slippage and roughness on gas flow in a nano tube model, we propose some more realistic parameters for simulating the gas flow in real mudrocks to study the flow mechanics, and to calculate the apparent directional permeability. The results show: 1) the simulated porosities (7.66% for S62H and 2.58% for S62V) are close to measured porosities (5.00% for S62H and 1.76% for S62V); 2) the estimated apparent permeability of S62H is 0.032 mD, which is close to the measured permeability of 0.02 mD; 3) the apparent directional permeability of S62V is not able to be estimated because the identified pores of subsamples are not connected in any direction with the image resolution of 65 nm/voxel; 4) the permeability anisotropy of S62H is clearly observed through the velocity field visualization and calculated permeability values; 5) the characteristics of pore geometry, flow velocity distribution and transport properties can be captured using DRP and the PLBM is an effective way to simulate complex gas flow in kerogen pores and estimate the apparent directional permeability. (C) 2017 Elsevier B.V. All rights reserved.