Moho structure provides important clues for understanding crustal structure, isostatic state and magmatic flux from mantle to surface. Across-basin Moho structure of the South China Sea (SCS) is important for understanding crustal evolution mechanisms of both continental break-up and seafloor spreading processes. Southwest Sub-basin (SWSB) opened up the latest and has the closest continental margins, making it the best to study the across-basin structure. Multichannel seismic (MCS) reflection data of line NH973-1 that crosses SWSB in NW-SE direction were reprocessed in order to image Moho structure. In MCS data, Moho reflectors are observed in places, which were not revealed in prior researches. The Moho generally shows symmetric structure on both sides of the central rift valley (CRV) and with variations in crustal thickness. Around CRV, the Moho is 2 seconds depth in two-way travel time (TWTT) beneath the igneous basement, which corresponds to 7 km depth, indicating normal oceanic crustal accretion during the ending of seafloor spreading. Close to the continent-ocean boundary (COB), the Moho becomes shallow to 1 second depth in TWTT (3.5 km), implying strong crustal thinning towards the continent, probably because of poor magma supply at the beginning of seafloor spreading. At south COB, the Moho depth under the crust almost reaches zero, which could be explained as a result of exhumed mantle. In addition, two low-angle, deep-penetrating normal faults are observed at south COB. The faults cut across the Moho into the upper mantle, which may be attributed to lithospheric hyper-stretching at COB during continental break-up.