A molecular dynamics simulation was performed to study the microstructure and void distribution in amorphous SiO2. Models were prepared at six temperatures and three densities. The microstructure of the simulated models was analyzed through partial distribution functions, coordination number, and bond-angle distribution. Two void aggregations were considered: void clusters (VCs) and void tubes (VTs). The calculation results showed several very large VCs with volumes as much as six times larger than that of a Si atom. A large VT, being the aggregation of 77% of all voids, was found in models and served as a fast diffusion path for O atoms. A weak change in short-range order as well as in behavior of void aggregation with temperature was observed. Furthermore, it was demonstrated that the large voids are “native” vacancies, whose concentration is independent of temperature. With an increase in system density, the void size became smaller and the void number became larger.