The inconsistency of the NS-trending fracture zones and the NW-SE-oriented extension during the latest spreading stage remains to be a problem in understanding the evolution of the South China Sea (SCS). Expedition 349 of the International Ocean Discovery Program (IODP) successfully drilled and cored five sites (Sites U1431-1435) close to the relict spreading centers and to the continent-ocean transition zone (COT), providing critical information on the spreading process. We analyzed macrostructures (over 300 fractures, veins, and slickensides) identifiable from the basalt and consolidated sediment samples. Compared with post-spreading volcanism, seismic interpretation, and focal mechanisms, as well as new-acquired free-air gravity anomaly and magnetic anomaly data, the latest spreading history of the SCS was explored. Post-spreading consolidated sediments are dominated by WNW- and nearly EW-trending planes with slickensides, consistent with the orientation distribution of the long axes of post-spreading volcanism, which suggests a relationship with the South China Sea eastward-subduction toward the Luzon Arc. The fractures and veins in the basalt oriented differently from the slickenside-bearing planes in sedimentary sequences, suggesting a NS-trending syn-spreading tendency. Magnetic anomalies suggest that the latest East Sub-basin’s relict ridge (ERR) may coincide with the trace of the seamount chain and trend roughly EW, where lower P-wave velocity in the upper crust was detected by Ocean Bottom Seismometer (OBS) experiments. The NS-trending Zhongnan–Liyue Fracture Zone (ZFZ) connects the East and Southwest relict ridges and was conjectured to be a fracture zone (relict transform faults). Although this tectonic event lasted only for a very short period of time, it was recorded by macrostructures at Site U1431 and U1433 accurately. These results resolve the previously identified inconsistencies and reveal for the first time the existence of latest NS spreading in this area. This study also provides a new angle to elucidate the kinematics of sea basin evolution through joint analysis of macro-scale structure and larger scale geophysical data.