The Liyue basin in the northeast of the southern margin of South China Sea (SCS) experienced complex tectonic evolution in Cenozoic, resulting in the differences of basin structures in different periods. Using abundant 2D seismic data and structural and stratigraphic analysis, this paper studied the evolution and transition process of basin structure, and their response to the complicated dynamic background of the South Sea region. The results show that controlled by the NNE, NEE, NWand nearlyEWtrending fault systems, the Liyue basin is characterized by two depressions (South Depression and North Depression) and one uplift (namely, the Central Uplift). Two regional angular unconformities T70 and T50 unconformities divide into the Cenozoic stratigraphy into three layers, continental rifting layer, drift rifting layer and forelanddepression layer. They responded to a series of reconstruction events of peripheral plates, such as Pacific plate subduction, IndiaEurasia plate collision, new South Sea expansion, ancient South Sea perish, and the Philippine Sea plate wedge, etc. The structural evolution of the Liyue basin experienced three stages, continental episodic rifting stage with the basin structure controlled by NNEand NEEtrending faults and the Southern Depression connected with the Northern Depression; drift rifting stage with the basin controlled by NNEand NWtrending faults and the newly formed Central Uplift separating the Southern Depression from the Northern Depression; forelanddepression stage with the basin shown as a foreland basin structure and quick depression deposition. The characteristics and evolution of basin structure were closely related to the complex dynamic background and recorded the response in the southern margin of SCS to the tectonic events, including the convergence of the Pacific, Eurasian and IndianAustralian plates, the protoSCS subduction, seafloorspreading of SCS and rotation of Philippine Sea Plate.