The structure of hydrous amorphous SiO2 is fundamental in order to investigate the effects of water on the physicochemical properties of oxide glasses and magma. The hydrous SiO2 glass with 13 wt.% D2O was synthesized under high-pressure and high-temperature conditions and its structure was investigated by small angle X-ray scattering, X-ray diffraction, and neutron diffraction experiments at pressures of up to 10 GPa and room temperature. This hydrous glass is separated into two phases: a major phase rich in SiO2 and a minor phase rich in D2O molecules distributed as small domains with dimensions of less than 100 Å. Medium-range order of the hydrous glass shrinks compared to the anhydrous SiO2 glass by disruption of SiO4 linkage due to the formation of Si–OD deuterioxyl, while the response of its structure to pressure is almost the same as that of the anhydrous SiO2 glass. Most of D2O molecules are in the small domains and hardly penetrate into the void space in the ring consisting of SiO4 tetrahedra.