Mega-pockmarks, which can reach a few kilometers in width and a few hundred meters in depth, and associated fluid escape features in the Northern Zhongjiannan Basin, South China Sea, have received much attention in the recent years, due to their large variety of morphologies and sizes. In this work, an integrated interpretation of detailed multibeam bathymetry, conventional multi-channel seismic reflection and seismic oceanography sections covering the northern Zhongjiannan Basin, South China Sea, are used to image the seafloor morphology, the subsurface geology and the water column, in order to better understand the geological and oceanographic controls on the formation and evolution of the widespread fluid escape features in this region. Regional uplift and volcanism took place in this area near the Palaeogene–Neogene boundary and, during the Neogene–Quaternary post-rift thermal subsidence period, differential subsidence and diapirism deformed the overlying kilometer-scale successions. Mainly after the Miocene, focused flow of fluids originated at depth occurred along gas pipes, polygonal faults, tapered reflectors and faults into the shallow sediments, resulting in intense fluid blowouts and complex fluid escape structures on the seafloor. Our results show that elongated pockmarks, pockmark gullies and gullies in the northern slope are generally controlled by underlying buried channels and gullies. However, pockmark gullies and gullies in the southern slope are controlled by gravity sliding/slumping, along with crescent pockmarks developing parallel to water depth contours. To varying degrees, intense fluid escape activities associated with mud diapirism and gas escape in the study area resulted in mud extrusion and the formation of mud volcanoes, complex seabed morphologies and irregular pockmarks. Mega-pockmarks, collapse structures and blind valleys have formed at the apexes of tectonic uplifts related to volcanism and above basement highs, which suggests that these processes played a role in creating pathways for fluid escape. Bottom currents associated with the South China Sea Western Boundary Current, imaged here for the first time with the seismic oceanographic method, mainly flow to the south, and erode the seafloor, making pockmark walls and slopes of gullies and channels in the north steeper than those in the south. Some fluid escape structures, such as the mega-pockmarks and pockmark gullies, are buried by sediment transported by the bottom currents. Turbidity currents flowing downslope along the long pockmark gullies also erode the seafloor and make the NW slopes of the mud volcanoes less steep than those in the SE. Eddies imaged by the seismic sections may also play a role in transporting sediment to the deep sea in this area. Some of the reported fluid escape structures are still active, as indicated by the fluid pathways that reach the seafloor and plumes in the water column imaged by the seismic sections.