Oxygen vacancies have proven to induce various and important effects on the properties of materials. In the present work, the thermodynamic stabilities and electronic properties of oxygen vacancies (Ov) on the SrTiO3 (STO)(001) surface and at the Au/STO(001) interface are systematically investigated by means of first-principles calculations. Both the SrO and TiO2 terminated (001) surfaces of STO are examined. It is found that the Ov located in the near-surface region of the two surfaces can be divided into three categories according to their properties: Ov in the surface atomic layer, Ov in the subsurface TiO2 atomic layers, and Ov in the subsurface SrO atomic layers. Counter-intuitively, for the SrO terminated surface the most stable site of Ov is in the first subsurface atomic layer. The Au metal in the Au/STO heterostructure significantly promotes the formation of Ov at and near the interface and thermodynamically promotes migration of Ov to the interfacial atomic layer. Furthermore, the interface Schottky barrier height is highly sensitive to both the concentration and position of Ov at the interface. These results are beneficial for the atomic-level understanding of the performance of STO-based photocatalysts and the rational design of more efficient ones.