The spatial and temporal interaction of rifting at the northern South China Sea (SCS) margin and shearing along Red River Fault Zone (RRFZ) is crucial to understanding the regional geodynamics. Their obscure relationship has led to controversial models for the origin of the Beibu Gulf basin within the northeast edge of the SCS. Newly released seismic-reflection data and well logs permit a new comprehensive analysis of the tectono-sedimentary history, which provides important constraints on the basin-forming history. Based on the interpretation of 3D multi-channel seismic data, we analyzed the seismic stratigraphy, fault development and tectonic subsidence, with additional confirmation from analogue modelling. The results suggest that several key unconformities separate the rifting history of North subbasins into three distinct phases. The syn-depositional faults and depocenters experienced a tectonic transition from NE- to NNE-orientated during the first two stages (65-30 Ma). The extensional structures were overprinted by the conjugate strike-slip faulting during stage III (30–23 Ma), as evidenced by the NEE-trending predominant faults and reactivation of NW-trending blind faults. Together with other regional geologic records and plate reconstruction history, we propose an updated view of the region's tectonic history. The NE-trending rift system initiated at the beginning of the Cenozoic. The Izanagi-Pacific mid-ocean ridge subduction induced a regional change of stress field to become north-south stretching that caused a tectonic transition of the basin. Influenced by the regional shearing activity of the RRFZ as well as additional north-south stretching, the basin was reworked by widespread strike-slip deformation. We therefore emphasize that while the basin's overall architecture was defined by the development of NE-trending rifts, both reconfiguration of the stress field acting on pre-existing faults and strike-slip reactivation of blind faults led to the basin's current intricate structure.