Traditional bathymetry inversion methods that rely on an altimetry-derived gravity anomaly (GA) and/or a vertical gravity gradient anomaly (VGG) have been widely used for bathymetry prediction in the South China Sea. However, few studies attempt new methods to combine multisource gravity data to improve the accuracy of the bathymetry. In this study, we introduce a fully connected deep neural network (FC-DNN) to merge GA, VGG, and the deflection of vertical (DOV) to predict the bathymetry in the South China Sea. Single beam sounding depths were used as sample data for neural network training. Independent shipboard depths and GEBCO2023, topo_25.1, and ETOPO2022 models were applied as validation data. The assessment results showed that the FC-DNN model reached a high precision level with an STD of 49.20 m. More than 70% of the differences between the FC-DNN bathymetric model and other depth models were less than 100 m. Furthermore, the spectral analysis results showed that the FC-DNN bathymetry model has stronger energy in medium and short wavelengths than other models, which indicates that additional gravity field element DOVs can recover richer topographic signals in those particular bands.