The central depression of the Qiongdongnan Basin can be divided into the eastern and western sub-basins by the Lingshui–Songnan paleo-uplift. To the northwest, the orientation of the faults turns from NE, to EW, and later to NW; In the southwest, the orientation of the faults turns from NE, to NNE, and then to NW, making the central depression much wider towards the west. In the eastern ... [Show full abstract] sub-basin, the NE-striking faults and the EW-striking faults made up an echelon, making the central depression turn wider towards the east. Fault activity rates indicate that faulting spreads gradually from both the east and west sides to the middle of the basin. Hence, extensional stress in the eastern sub-basin may be related to the South China Sea spreading system, whereas the western sub-basin was more under the effect of the activity of the Red River Fault. The extreme crustal stretching in the eastern sub-basin was probably related to magmatic setting. It seems that there are three periods of magmatic events that occurred in the eastern sub-basin. In the eastern part of the southern depression, the deformed strata indicate that the magma may have intruded into the strata along faults around T60 (23.3 Ma). The second magmatic event occurred earlier than 10.5 Ma, which induced the accelerated subsidence. The final magmatic event commenced later than 10 Ma, which led to today’s high heat flow. As for the western sub-basin, the crust thickened southward, and there seemed to be a southeastward lower crustal flow, which happened during continental breakup which was possibly superimposed by a later lower crustal flow induced by the isostatic compensation of massive sedimentation caused by the right lateral slipping of the Red River Fault. Under the huge thick sediment, super pressure developed in the western sub-basin. In summary, the eastern sub-basin was mainly affected by the South China Sea spreading system and a magma setting, whereas the western sub-basin had a closer relationship with the Indo-China extrusion system.