The nanostructure of Six(SiO2)1–x films deposited on quartz substrate, where x varies from 0 to 1, was determined by high-resolution transmission electron microscopy in the sample regions with x ≈ 0.1, 0.2, 0.5, and 0.75. In the Si0.5(SiO2)0.5 region, the formation of a Si nanocrystallite network was established. At high concentrations of Si nanocrystallites, nanotwins and stacking faults occurred in the crystallites. Large Si crystallites appeared at x ⩾ 0.5 in the quartz substrate under the interface, while the film presented nanopores over the interface. The mechanisms for the formation of the nanocrystallites were discussed and correlated with the film properties.