The crustal structures of the continent-ocean transition (COT) zone and oceanic domain are key to revealing the tectono-magmatic evolution from rift to drift and the following seafloor spreading. We present a comprehensive study of deep seismic reflection imaging and tomographic inversion of a wide-angle seismic line that runs across the COT and extinct spreading center of the Southwest Subbasin (SWSB) in the South China Sea. We revealed a low velocity (<3 km/s) region in the shallow upper crust of the Longmen seamount, which may represent serpentinized mud or volcanoclastic. The mature oceanic crust is ca. 4–6 km thick with high-velocity bodies (7.2–7.5 km/s) overlapping the Moho, reflecting relatively rich magmatic additions during seafloor spreading. Both the northern and southern COT segments exhibit a prominent long-wavelength high magnetic anomaly and syn-breakup volcano, indicating magmatic additions in the lower crust and lava flows with magma ascending along faults to the surfaces. However, the COT in the south is wider than that in the north. In addition, the southern COT is characterized by limited PmP reflections, well-developed rotated fault blocks and ocean-ward syn-rifting faults, and a low velocity (7.5–7.8 km/s) upper mantle, suggesting the southern COT is probably underlain by a local serpentinized mantle during continental lithosphere breakup. The differences between the southern and northern COTs on the origin of high velocity lower crustal layers and faulting styles implies asymmetric continental breakup processes in the SWSB.