Using regional geological, newly acquired 2D and 3D seismic, drilling and well log data, especially 2D long cable seismic profiles, the structure and stratigraphy in the deep-water area of Qiongdongnan Basin are interpreted. The geometry of No.2 fault system is also re-defined, which is an important fault in the central depression belt of the deep-water area in the Qiongdongnan Basin by employing the quantitative analysis techniques of fault activity and backstripping. Furthermore, the dynamical evolution of the No.2 fault system and its controls on the central depression belt are analyzed. This study indicates that the Qiongdongnan Basin was strongly influenced by the NW-trending tensile stress field during the Late Eocene. At this time, No.2 fault system initiated and was characterized by several discontinuous fault segments, which controlled a series small NE-trending fault basins. During the Oligocene, the regional extensional stress field changed from NW-SE to SN with the oceanic spreading of South China Sea, the early small faults started to grow along their strikes, eventually connected and merged as the listric shape of the No.2 fault system as observed today. No.2 fault detaches along the crustal Moho surface in the deep domain of the seismic profiles as a large-scale detachment fault. A large-scale rollover anticline formed in hanging wall of the detachment fault. There are a series of small fault basins in both limbs of the rollover anticline, showing that the early small basins were involved into fold deformation of the rollover anticline. Structurally, from west to east, the central depression belt is characterized by alternatively arranged graben and half-graben. The central depression belt of the Qiongdongnan Basin lies at the extension zone of the tip of the V-shaped northwestern ocean sub-basin of the South China Sea, its activity period is the same as the development period of the northwestern ocean sub-basin, furthermore the emplacement and eruption of magma that originated from the mantle below the Moho surface occurred at the region between Songnan-Baodao and Changchang sags, from east to west with the early-stage spreading of the South China Sea. Therefore, this study not only helps in depicting the structural features and evolution of the deep-water basin in the Qiongdongnan Basin, but also provides the geological and structural evidence for establishing a unified model of continental margin extension and oceanic spreading.