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Macrostructures preserved in deformed rocks are essential for the understanding of their evolution, especially when the deformation is weak and hard to discriminate in regional scale or purely through geophysical data. In order to resolve the inconsistency between NS trending fracture zones and NE oriented spreading fabrics of the South China Sea during the latest spreading stage, we analyzed macrostructures identifiable from the basalt and consolidated sediment samples of the Integrated Ocean Drilling Program (IODP) Sites U1431 and U1433. These two sites are close to the East and Southwest relict spreading ridges and provide critical information on the latest spreading stages. The structures in the basalt of both sites suggest two dominant orientations of NS and NE. At U1431, sediments show mainly WNW trending slickensides, different from that of basalt. At U1433, no structures were found in postspreading sediment. Thus, NE and NS trending structures in basalt are most possibly formed by seafloor spreading. Crosscutting relationship suggests that NE trending structures formed first, followed by NS and finally WNW trending structures. These observations are consistent with geophysical features. Magnetic anomalies and ocean bottom seismometer velocity suggest that the latest relict ridge of the East Subbasin coincides with the EW trending seamount chain. Located between the relict ridges of East and Southwest Subbasins, NS trending Zhongnan‐Liyue Fracture Zone had acted as the latest transform fault. Based on the above evidences, we proposed that the South China Sea may have experienced a short period of NS oriented spreading after earlier SE spreading. These results resolve the previous inconsistencies.