Abstract: Marine magnetic anomalies have two kinds of distribution patterns:the magnetic lineation and the magnetic quiet zone (MQZ). The MQZs show large-area magnetic anomalies with low value in magnetic anomaly maps. The MQZ in the northern South China Sea is located along the continent-ocean boundary (COB), to the south of high positive magnetic anomaly belt and the north of the magnetic lineation in the sea basin. We define the distribution range of the MQZ clearly according to the △T magnetic anomaly data, the free air gravity anomaly data and tectonic background information. We obtain the reduction to pole magnetic anomaly using a low magnetic latitude method and discuss the characteristics of gravity and magnetic field in the Northern South China Sea by the wavelet multi-scale decomposition method. We obtain the depth of the magnetic basement, the depth of the Curie isothermal interface, the thickness of the magnetic layer and the depth of Moho interface by the Parker inversion method. The inversion results show that the depth of Curie isothermal interface and the depth of Moho in the MQZ are shallow. The magnetic basement is deeper than surrounding areas. We infer that the thinning of the magnetic layer is the direct reason of the formation of the MQZ which has three causes.