A large number of seabed depressions, covering an area of 2500 km² in the Xisha Massif of the South China Sea, are investigated using newly collected high-resolution acoustic data. By analyzing the morphological features and seismic attributes of the focused fluid flow system, five geological structures are recognized and described in detail, including pockmarks, volcanic mounds, pipes, faults, and forced folds. Pockmarks and volcanic mounds occur as clustered groups and their distributions are related to two large-scale volcanic zones with chaotic seismic reflections. Pipes, characterized by disordered seismic reflections, mainly occur within the focused fluid flow zone (FFFZ) and directly link with the large-scale deep volcano and its surrounding areas. Faults and fractures mainly occur along pipes and extend to the seafloor, commonly presenting lateral walls of mega-pockmarks. Forced folds are primarily clustered above volcanic zones and commonly restricted between faults or pipes, characterized by sediment deformations as indicated in seismic profiles. By comprehensive analysis of the above observations and a simplified simulation model, the volcanism-induced hydrothermal fluid activities are argued herein to contribute to these focused fluid flow structures. In addition, traces of suspected submarine instability disasters such as landslides have been found in this sea area, and more observational data will be needed to determine whether seafloor fluid flow zones can be used as a predictor of seafloor instability in the future.