Marine magnetic lineations play important role in interpreting the age and spreading processes of the oceanic crust. However, it is difficult to identify magnetic lineations from sea surface observations in a deep and narrow low-latitude slow-spreading inactive ocean basin for many reasons, such as the highly filtered low-amplitude magnetic anomalies, highly oblique magnetization, contamination from narrow stripes, etc., which may hamper accurate lineation discrimination and identification. The spreading history of the Southwestern Sub-basin of the South China Sea (SW-SCS), which is located in such a low-latitude tectonic setting, has been debated for a long time. Near-seafloor deep-tow magnetic measurements provide high-resolution reversal records, making accurate lineation discrimination feasible. Corrections, including diurnal variation correction, regional field correction, and de-skewing, are explored. The results, calibrated with drill sites from the International Ocean Discovery Program (IODP) Expedition 349, show that the spreading ages of the SW-SCS range from ∼ 21 to 15 Ma (from C6A to C5B) and the full spreading rate ranges from 26 to 46 mm/yr, with an average rate of 37 mm/yr. Spreading was initially symmetric but later became asymmetric, with a rate differential reaching 10%. Combined with two seismic profiles, it is found that the roughness of the oceanic basement to the south of the extinct ridge is mainly influenced by faulted blocks, whereas to the north it is mainly influenced by magmatism. The RMS seafloor roughness is estimated to be 211 m in the south and 191 m in the north respectively. This indicates that SW-SCS seafloor spreading tends to be a transition type between axial high and axial low at the intermediate-slow spreading rate. There is a large valley in the spreading center, but the roughness far away from the center is low. the RMS basement roughness is obviously lower than that of the typical slow spreading oceanic basin. we conjecture that the larger than normal syn-spreading magma may be the reason for the low roughness. A long history of being subducted might be the deep-seated reason for all these behaviors where, and the mantle is rich in water and carbon.