Since the onset of the Cenozoic, the South China Sea has experienced complex plate interactions including peripheral plate collisions, the demise of the Paleo-South China Sea, and the subsequent opening of the modern basin. These processes produced three major types of sedimentary basins: extensional, strike-slip, and compressional. The Beikang Basin represents a typical extensional continental-margin rift basin that preserves the stratigraphic and sedimentary record of the transition from syn-rift to post-rift stages. Subsidence happened mainly during the post-rift stage. Five structural styles exist: extensional, compressional-inversion, strike-slip–extensional, magmatic, and diapiric. While the first three are fault-related, the last two are mainly controlled by the volcanic phases. Using a seismic-facies-to-sedimentary-system workflow, we delineate a tectono-stratigraphic framework, comprising five seismic facies, seven lithofacies, and eight depositional facies. This framework indicates that the Beikang Basin evolved through four major tectonic stages including initial rifting, inherited rifting, climax rifting, and post-rift thermal subsidence. Each stage has primary control on sediment supply and accommodation development. Our findings refine the basin’s tectono-sedimentary evolution and improve predictions for sediment distribution and hydrocarbon exploration in the underexplored Beikang Basin.