Rift basins in eastern and southern China host abundant oil and gas resources. But the complicated evolution and distribution of the faults are the key issues to be solved in future oil and gas exploration and development. Based on the structure interpretation of a large number of 3D seismic data and the generalized faulting model, this study selected the Nanpu Sag in the Bohai Bay Basin and the Weixinan Sag in the Beibuwan Basin as study examples so as to analyze and summarize the complicated fault system of basins in eastern and southern China. An extension strain ellipse was proposed to predict fault nature in extensional deformation zone. The results show that there are nine ways by which fault system complexity of rift basins in the east-south China are presented. They can be further summarized into three aspects, (1) variety of the fault strike and nature, (2) variable assemblages in the plane and profile, (3) complicated spatiotemporal relation of fault distribution and evolution. The fundamental reasons for complexity of the fault system are the distribution complexity of the preexisting faults and the superposition of extensional deformation in different directions (NWSE and near NS). The evolution of tectonic stress field in different basins and even in different parts of a basin shows great similarities, NWSE extension before 40Ma and northsouth extension since 38Ma. Therefore, the distribution and evolution of faults are mainly affected by the differences in the distribution of preexisting faults.