Qiongdongnan Basin, located in the northwest of the northern continental margin of the South China Sea, is a NNE extensional basin formed in the Cenozoic era. The fault trend, distribution direction of secondary depressions and tectonic styles show obvious differences between the eastern and the western zones. In this work, the influence of the orientation of the preexisting structure and basement properties of the Mesozoic structures on the tectonic evolution of Qiongdongnan basin is discussed by using physical simulation experiments. The experimental results indicate that:(1)the pre-existing structural orientation and the regional extension direction jointly control the fault strikes and structural styles of the rift basin. As a result, the fault system of Qiongdongnan Basin shows segmentation between the western and eastern zones. The differences of fault systems between the western and eastern zone have been formed during the first-rift stage(Tg-T80), while the later fault systems inherited and reformed from the first-rift stage. The pre-existing structure is the main controlling factor leading to the differential development of the eastern and western structures in the Qiongdongnan Basin. (2)the difference of basement strength has a great influence on the number of faults and the characteristics of topographical relief. The tectonic differential evolution between the eastern and western zones of Qiongdongnan Basin controlled by the basement strength, pre-existing structural orientation and stress direction.