We processed the raw multi-beam bathymetry data acquired in the central and northeastern part of the South China Sea by eliminating noise and abnormal water depth values caused by environmental factors, and a high resolution bathymetric map with a 20-m grid interval was constructed. Various scales of seafloor geomorphological features were identified from the data, including an image of Shenhu canyon, which is located in the northern continental margin of the South China Sea; submarine reticular dunes in the north of the Dongsha atoll; submarine parallel dunes in the northeast of the Dongsha atoll; and several seamounts in the southwest sub-basin and in the east sub-basin. In the processing step, various anomalies in the multi-beam bathymetry data were corrected. The optimal swath filtering and surface filtering methods were chosen for different scales of seafloor topography in order to restore the true geomorphological features. For the large-scale features with abrupt elevation changes, such as seamounts (heights of ~111–778 m) and submarine canyons (incision height of ~90–230 m), we applied swath filtering to remove noise from the full water depth range of the data, and then surface filtering to remove small noises in the local areas. For the reticular dunes and parallel dunes (heights of ~2–32 m), we applied only surface filtering to refine the data. Based on the geometries of the geomorphological features with different scales, the marine hydrodynamic conditions, and the regional structure in the local areas, we propose that the Shenhu submarine canyon was formed by turbidity current erosion during the Sag subsidence and the sediment collapse. The submarine reticular dunes in the north of the Dongsha atoll were built by the multi-direction dominant currents caused by the previously recognised internal solitary waves around the Dongsha atoll. The submarine parallel dunes in the northeast of the Dongsha atoll were built by the repeated washing of sediments with the influence of the tidal currents and internal solitary waves. The conical, linear and irregular seamounts identified from the bathymetry data were formed during the spreading of the southwest sub-basin and the east sub-basin. The identified seamounts in the multi-beam bathymetry data are correlated to deep magmatic activities, the Zhongnan transform fault and the NE-trending faults.