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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.