Abstract: The deep-water area of the northern continental margin in the South China Sea, a potential area with unique geological setting and excellent geological conditions for gas accumulation, has got great attention from scholars both at home and abroad. It is required to solve the basic geological problems in the early stage of the deep-water exploration, which has high risk and high economic threshold. The structural geology of the deep-water basins is no doubt one of most important geological problems to be solved. The Eastern Sag belt of the Qiongdongnan Basin, i.e. the Songnan-Baodao-Changchang Sag, is located in the east part of the Central Depression of the Qiongdongnan Basin, where complicated fault systems dominate. Our study suggests that: (1) the Eastern Sag belt of the Qiongdongnan Basin is in a shape of parallelogram in a plane view, with changes from a half-graben to an asymmetric graben to a half-graben in the section from west to east. (2) The fracture system can be subdivided into three types, i.e. the boundary fault in the border, the depositional fault in the center and the transfer fault in between. (3) These faults are developed and constrained by the joint action of the subduction of the Pacific Plate and the spreading of the South China Sea in Paleogene. As the tectonic stress field switched from NW-SE to NS, the structural evolution of the region could be divided into three phases. In the phase of pre-Eocene (~32 Ma), the boundary fault system with a NE-SW strike was controlled by the extensional stress in NW-SE direction; In the phase of Late- Eocene—early Oligocene (32-26 Ma), the growth fault system with a NWW-SEE strike was controlled by the extension in SN direction; In the phase after Late Oligocene(26~ Ma), the fault systems in NE-SW and NWW-SEE direction inherited from the former as the decrease in the regional extension and the spreading of the South China Sea. The movement of faults was accelerated while the Yangcheng and Lingshui Formations were deposited, that controlled the mass deposition of the Yangcheng and Lingshui Formations and benefited the sedimentation of source rocks. (4) The structural traps in shapes of fault nose and fault block developed in the inner-sag uplift can be considered as the most optimum exploration targets.