We made a systematic investigation on major structures and tectonic units in the South China Sea basin based on a large magnetic and seismic data set. For enhanced magnetic data interpretation, we carried out various data reduction procedures, including upward continuation, reduction to the pole, 3D analytic signal and power spectrum analyses, and magnetic depth estimation. Magnetic data suggest that the South China Sea basin can be divided into five magnetic zones, each with a unique magnetic pattern. Zone A corresponds roughly to the area between Taiwan Island and a relict transform fault, zone B is roughly a circular feature between the relict transform fault and the northwest sub-basin, and zones C, D, and E are the northwest sub-basin, the east sub-basin, and the southwest sub-basin, respectively. This complexity in basement magnetization suggests that the South China Sea evolved from multiple stages of opening under different tectonic settings. Magnetic reduction also fosters improved interpretation on continental margin structures, such as Mesozoic and Cenozoic sedimentary basins and the offshore south China magnetic anomaly. We also present, for the first time, interpretations of three new 2D reflection seismic traverses, which are of ∼2,000 km in total length and across all five magnetic zones. Integration of magnetic and seismic data enables us to gain a better 3D mapping on the basin structures. It is shown that the transition from the southwest sub-basin to the east sub-basin is characterized by a major ridge formed probably along a pre-existing fracture zone, and by a group of primarily west-dipping faults forming an exact magnetic boundary between zones D and E. The northwest sub-basin has the deepest basement among the three main sub-basins (i.e., the northwest sub-basin, the southwest sub-basin, and the east sub-basin). Our seismic data also reveal a strongly faulted continent–ocean transition zone of about 100 km wide, which may become wider and dominated with magmatism or transit to an oceanic crust further to the northeast.