A great amount of new S-wave data has been combined to image the mantle structure down to lower mantle depth near the southeastern margin of Eurasia and understand the tectonics in South China since the Mesozoic. Our results reveal a large-scale structure beneath the South China Sea, with a prominent, broad low-velocity feature of at least 1500-km wide in and below the mantle transition zone (MTZ) and a pronounced low-velocity feature of nearly 500-km wide in the lowermost mantle. Together these features may represent the head-and-tail of an upwelling mantle plume that has interacted with and deformed by the subducting plates in the region. The Andaman–Sumatra plate is seen subducting steeply without stagnation in the MTZ over the large-scale low-velocity structure, suggesting that the upwelling mantle may have exerted significant influence on the overlying plate tectonics. Our results suggest a long-term extensional regime near the southeastern margin of Eurasia, which may help to understand the formation of the large-scale intra-plate magmatism and mineralization with accumulation of huge amount of rare metal elements in South China during the Mesozoic, and the continental breakup, the southeastward extrusion of Indochina, and the opening of the South China Sea during the Cenozoic.