The paleoceanography and deep-water circulation process of the South China Sea (SCS) is still poorly understood. We have evaluated multibeam bathymetry and multichannel seismic reflection data acquired by Guangzhou Marine Geological Survey in recent years, and we investigate the characteristics, distribution, and generation mechanism of submarine seabed gullies and mega-pockmarks in the northern Zhongjiannan Basin of the SCS. Our data reveal that there are northwest–southeast-trending gullies and randomly or linearly arraying mega-pockmarks in the northern depression of the Zhongjiannan Basin. Gullies are 1 km or more in width and tens of kilometers in length. The long-axis diameter for the largest mega-pockmarks can reach up to 4293 m. The mega-pockmarks found in the west block of the northern depression are the manifestation of focused fluid flow migrating along shallow inclined faults induced by slumps that reached the seabed. Gullies are trending southeast and perpendicular to the contours of the continental slope, suggesting that gravity flows have played an important role in the evolution of gullies. Our data demonstrate that the gullies have a close relationship with mega-pockmarks, and that they were formed through the interaction of intense focused fluid flow and gravity flows. The pockmarks formed first, subsequently growing in size and number under the effect of subsurface fluid flows. The southeastward moving gravity flow caused discrete pockmarks to coalesce and form immature gullies. After being fully converged, gullies finally become smooth-bottomed and matured. Because gullies and mega-pockmarks are the manifestation of the geologic process of fluid escape at the seabed, they should be taken into account when assessing the potential for gas hydrates and seafloor instability.