Abstract: There are many small and medium-sized Cenozoic sedimentary basins in the southern South China Sea, such as the Nanweixi Basin, the Beikang Basin, the Liyue Basin, the Zengmu Basin, the Nansha Trough, the Brunei-Sabah Basin, the Northwest Palawan Basin and other basins from north to south. In general, NE-trending faults control the formation of the half grabens with faulting in the north and overlapping in the south. However, single grabens are mainly developed in the northern continental slope, while two-layered basins developed in the south of the region, of which the lower layer is the graben and the upper layer the imbricated nappes. According to the nature of main controlling faults and the transition of the basins at different evolutionary stages, these basins can be divided into three groups:the rift basin group (the Nanweixi, Beikang and Liyue basins), the rift-pull-apart-foreland superimposed basin group (the Zengmu basin) and the rift-foreland basin group (the Nansha Trough, Brunei-Sabah, the Northwest Palawan basins). The formation of these basin groups is closely related to major marginal faults of the basins and secondary faults in the sub-basins. Based on the nature of the faults, the basin-controlling fault belts can be subdivided into three types:tensile, shear and compressional, including the extensional fault belt in the northern edge of the Nansha Trough, the strike-slip fault belts at the west edge of the Wanan Basin and the Lupar and the Tingjia-Lee Jun Fault belts, and the thrust fault belt in the southern edge of the Nansha Trough. Tectonic events which happened in southern South China Sea, such as the South China Sea Movement in Oligocene and the Nansha Movement in the Middle Miocene, affected the basins to various degrees. As the result, there was the inversion from a rift basin/pull-apart basin to a marine foreland basin, as well as the inversion of fault belts from normal faults to reverse faults or strike-slip faults. The kinetic mechanism of the basin groups varies in different stages. In the early stage, it may be related to the continental rifting of the southeast edge of the Eurasia continent, and the subduction and dragging of the Paleo-South China Sea slab resulted in the splitting of southern South China Sea from the South China continent, and then, half garbens formed with faulting in the north and overlapping in the south. In the later period (about 16 Ma), the north-directed imbricated thrust nappes propagated forward in the southern South China Sea due to the collision of the southern Australian Plate to the northern Eurasian Plate, which resulted in the transition of basin types and the counterclockwise rotation of the Borneo Block.