Water is the most common volatile component inside the Earth. A substantial amount of water can be carried down to the interior of the Earth by subducting plates. However, how the subducted water evolves after the subducting slab breaks off remains poorly understood. Here we use the data from a passive seismic experiment using ocean bottom seismometers (OBSs) together with the land stations to determine the high-resolution, three-dimensional seismic structure of the Southwest Sub-basin (SWSB) of the South China Sea (SCS). At depths below 40 km, the mantle shear velocity (Vsv) beneath the northern side of the SWSB is similar to that of the conventional oceanic pyrolite mantle, but roughly 3% shear-velocity reduction is found beneath the southern side of the SWSB. Results of thermal dynamic modeling reveal that the observed shear-velocity reduction could be explained by the presence of 150–300 ppm of water and 5–10% of lower continental crust. The inferred high-water content at the southern side of the SWSB is consistent with a model in which the Proto-SCS plate subducted southward prior to and during the formation of the SCS basin, releasing water into the upper mantle of the SWSB.