Pore scale and the pore structure have significant effects on mass transfer properties through the porous media. In this article the effects of nanoscale pore structure (0.01 < Kn < 0.1) on permeability and permeability damage were studied by the GPU enhanced Multiple-Relaxation-Time (MRT) Lattice Boltzmann Model (LBM). Six mono-sized-bead packed nanoscale pores and six two-sized-bead packed same porosity different structure (SPDS) nanoscale pores were made to analyze scale and pore structure effects on permeability. The water predicted permeability and air predicted permeability in these nanoscale pores were estimated, and a modified slip boundary condition was implemented to mimic rarified gas effect in this scale. Simulation results are coherent with Klinkenberg effect that air predicted permeability is larger than water predicted permeability in every pore sample. Further analyses showed that pore dimension evenness degree (PDED, the ratio of max pore diameter to min pore diameter) is an essential factor of permeability. Larger PDED increases pore structure complexity, total surface area and tortuosity, but decreases permeability; smaller PDED has opposite effects. PDED is a new pore structure parameter presented in this article. GPU speed up results showed that CUDA parallel significantly accelerated calculation. The highest speed up ratio of CUDA parallel to single CPU was 468. (C) 2017 Elsevier Ltd. All rights reserved.