In view of the fact that the northern South China Sea has complex geological structure, well-developed igneous rocks, and serious multiple wave interference, the authors used marine gravity and magnetic survey data, chose the United States FUGRO-LCT gravity magnetic seismic integrated interpretation system as the study platform in combination with seismic data to build a reasonable 2.5D geological-geophysical initial model and conduct synchronous gravity and magnetic forward and inversion calculation. According to the results of fitting modified seismic reflection fuzzy regional calibration position, the authors determined the deep formation properties and the structure of the crust. The results show that the Mesozoic formation density of the northeastern South China Sea is generally 2.40~2.57 g/cm³, and the density of some igneous rocks is less than that of Mesozoic sedimentary rocks. Some areas have magnetism, caused by sedimentary rock interbedded with igneous rock. Dongsha Island of the south slope and the basin at the junction of crustal structure are weak areas, where there may be Pre-Mesozoic strata. The region from the southern uplift area to the northeast area of the central basin remains the excessive crust.