In this paper, we introduced charge transfer of Si and O atoms for molecular dynamics simulation of SiO2. The effect of atomic charge transfer on vitreous silica simulation was investigated by Morse potential. Results show that atomic charge transfer not only affects the density of vitreous silica models, but also affects the interatomic nearest distance directly. The result comparison between the NPT and NVT ensembles indicates that the interatomic nearest-distances in the two ensembles are similar with the same atomic charge transfer but larger voids are found in the NVT model, which can account for the void structure in real glass. We clarify why simulations overestimate densities compared to experimental data. We also describe a better method of molecular dynamics modeling for vitreous silica. This method resolves the conflict between maintaining the interatomic nearest distance and keeping the model density as the atomic charge transfer changes. It also describes the long-range disordered structure of density non-uniformity and larger voids well. Furthermore, the result of atomic self-diffusion coefficient shows the significance of a larger void structure in the study of diffusion properties in vitreous silica.