The Zhongnan Fault Zone (ZFZ) is a large-scale tectonic belt in the South China Sea (SCS) oceanic basin and plays an important role in the formation and evolution of the basin. Despite numerous studies over the past few decades, debates persist regarding its location, orientation, nature, time of activity, and genesis. In this study, we evaluate our findings on the characteristics and origin of the fault zone through an integrated analysis of multibeam bathymetric and 2D multichannel seismic data. Our results reveal the ZFZ as a fault zone approximately 400 km long and 50–90 km wide, situated between the east subbasin (ESB) and southwest subbasin (SWSB) of the SCS. The fault zone is oriented N8°W, roughly perpendicular to and laterally displacing the relict spreading center and related spreading lineaments. Bounded by discontinuous linear seamounts, the fault zone comprises two V-shaped subparallel pull-apart basins and a separating basement high. Steeply dipping (>60°) normal basement-involved faults bound these pull-apart basins, forming typical negative flower structures. Numerous northeast-oriented en-echelon linear bathymetric highs within the fault zone are identified as secondary antithetic shears (P′ shears). These shears are characterized by their orientation relative to the principal displacement zones defined along the pull-apart basins. The ZFZ exhibits differences from the adjacent subbasins in water depth, basement burial, stratal thickness, and seismic stratigraphic characteristics. Five seismic sequences (S1–S5 upward) in the ZFZ and nearby ESB and SWSB are defined, dating to the Early Miocene synspreading (S1) and the Middle Miocene to Recent postspreading (S2–S5) stages, respectively. The difficulty in correlating seismic facies in sequences S1–S3, compared with the comparable seismic facies in sequences S4–S5 between the ZFZ and adjacent subbasins, suggests a horizontal displacement during the synspreading and early postspreading stages. We propose that the ZFZ functioned as a right-lateral transform fault zone during the synspreading period (the Early Miocene, approximately 24–16 Ma) of the SWSB and transitioned into a left-lateral strike-slip fault zone during the successive early postspreading period (the Middle-Late Miocene, approximately 16–5.3 Ma).