Pore structures of microporous silica membranes, and the relationship between membrane structural characteristics and gas permeation properties were studied by molecular dynamics (MD) simulation. Virtual SiO(2) membranes were prepared by the melt-quench procedure utilizing Born-Mayer-Huggines (BMH) pair potential and Stillinger-Weber (SW) three-body interactions. In this study, two types of virtual SiO(2) membrane models were prepared: a network pore model formed by silica polymers; and a bimodal pore model consisting of network pores and penetrating pores, which simulated an inter-particle pore. Gas permeation simulations were conducted using a dual control plane non-equilibrium molecular dynamics (DCP-NEMD) method. Helium and CO(2) were adopted as permeating gas species, and their permeabilities were calculated at temperatures from 300 to 800 K. In the case of the network model, permeation of CO(2) could not be observed, and helium permeation characteristics were in good agreement with experimental data. These results showed the qualitative validity of the network pore model prepared in this study. In the case of bimodal pore model, permeation of CO(2) could be observed, so this result indicated the existence of an inter-particle pore effect on gas permeation properties. In addition, CO(2) permeation characteristics were in agreement with experimental data, thus indicating the qualitative validity of the network pore model and penetrating pore model. However, the simulated permeabilities of helium and CO(2) by the bimodal pore model were larger than those previously reported for actual silica membranes. The bimodal pore model prepared in this study underestimates the ratio of network pore area per inter-particle pore, since the simulated permeability of each gas through the bimodal pore model could be approximated to experimental data by increasing the ratio of network pore area per inter-particle pore. Optimization of the virtual silica membrane area showed that one inter-particle pore existed per square with side length of about 8-11.5 nm. Such a valuable finding about the microstructure of a silica membrane as the ratio of "network pore area/inter-particle pore" could be obtained by using molecular dynamics simulation.