The northeastern continental margin of the South China Sea is very important for studying the deep structure of the South China Sea. Because the magnetic survey data in this area is affected by the oblique magnetization of the middle and low latitudes, this paper adopts the magnetic inversion method with variable inclination and declination studied by predecessors, and proves the effectiveness of the method through model tests. Then through the three-dimension magnetic inversion of the regional intensity of magnetic anomaly data in the northeast of the South China Sea, we extracted the characteristics of the magnetic layer thickness distribution in the study area. In addition, combined with the ocean-bottom seismology profiles, we analyzed the genesis of the high-velocity layer in the low crust. It is believed that the formation of the low crustal high-velocity layer is closely related to the magma underplating of the upper mantle.

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