The distribution of oil and gas resources in the South China Sea and adjacent areas is closely related to the structural pattern that helped to define the controlling effect of deep processes on oil-bearing basins. Igneous rocks can record important information from deep processes. Deep structures such as faults, basin uplift and depression, Cenozoic basement and magnetic basement are all the results of energy exchange within the earth. The study of the relationship between igneous rocks and deep structures is of great significance for the study of the South China Sea. By using the minimum curvature potential field separation technique and the correlation analysis technique of gravitational and magnetic anomalies, the fusion of gravitational and magnetic data reflecting igneous rocks can be obtained, through which the igneous rocks with high susceptibility/high density or high susceptibility/low density can be identified. In this study area, igneous rocks do not develop in the Yinggehai basin, Qiongdongnan basin, Zengmu basin and Brunei-Sabah basin, whilst igneous rocks with high susceptibility/high density or high susceptibility/low density are widely-developed in other basins. In undeveloped igneous areas, faults are also undeveloped, the Cenozoic thickness is greater, the magnetic basement depth is greater and the Cenozoic thickness is highly positively correlated with the magnetic basement depth. In igneously developed regions, the distribution pattern of the Qiongtai block is mainly controlled by primary faults, while the distribution of the Zhongxisha block, Xunta block and Yongshu-Taiping block is mainly controlled by secondary faults, the Cenozoic thickness having a low correlation with the depth of the magnetic basement.