Based on the study of the crustal structure, the authors point out that there exits a high velocity layer in the lower crust of northeast South China Sea, which distributes around continental shelf and rifted continental slope from 112°E ~ 120° E , 19° N ~ 22°N in NEE strike. The high velocity layer can reach as thick as 8 km according to the OBS data, its thickness reduces from the continental shelf to the South China Sea ocean basin gradually. From multidisciplinary analysis, the high velocity layer in lower crust is interpreted as magmatic underplating. It emplaced almost simultaneous with the South China Sea spreading around 30Ma, and gave rise to crust uplifting and erosion of the study area.