<p>Beikang Basin (BKB) and Nan’an Basin (NAB), which are located on the southwestern continental margin of the South China Sea (SCS), preserve records of tectonic deformation and sedimentary processes, spanning from the subduction of the proto-SCS and continental rifting to the seafloor spreading of the SCS. These basins offer a major geological archive for understanding the evolution of the SCS margin. This study integrates 2D seismic interpretation, borehole data, and balanced cross-section restoration to analyze the structural architecture, fault kinematics, and spatiotemporal migration of rifting in these basins. Our results reveal distinct structural styles: the BKB is dominated by WNW–ESE, NE–SW, and NNE–SSW trending faults that define a series of half-grabens, whereas the NAB is primarily controlled by NE–SW and ENE–WSW trending faults, forming a composite graben–half-graben system. Fault activity analysis indicates that NNE- and NE-trending faults dominated the early rifting stage, followed by a progressive intensification and eventual predominance of WNW- and ENE-trending faults during the late stage. Balanced cross-section restoration further delineates the Cenozoic tectonic evolution of the southwestern SCS margin into three distinct phases: initial rifting, intense rifting, and thermal subsidence. Crucially, our analysis of fault activity and breakup unconformities reveals a systematic NE-to-SW migration of rifting activity across the basins. This spatiotemporal pattern closely corresponds to the southwestward progression of SCS seafloor spreading. These findings provide direct structural constraints on the tectonic evolution of the southwestern SCS margin and offer valuable insights for deepwater hydrocarbon exploration.</p>