The continental margins of the southwest subbasin in the South China Sea mark a unique transition from multi-stages magma-poor continental rifting to seafloor spreading. We used reflection and refraction profiles across the margins to investigate the rifting process of the crust. Combining with the other seismic profiles acquired earlier, we focused on the comparative geological interpretation from the result of multichannel seismic analysis and wide-angle seismic tomography. Our result provides the evidence of upper crustal layer with abundant fractures below the acoustic basement with a P-wave velocity from 4.0 to 5.5 km s?1. It indicates extensive deformation of the brittle crust during the continental rifting and can make a good explanation for the observed extension discrepancy in the rift margins of the South China Sea. The seismic chronostratigraphic result shows the possibility of the intra-continental extension center stayed focused for quite a long time in Eocene. Additionally, our evidence suggested that continental margin of the southwest subbasin had experienced at least three rifting stages and the existence of the rigid blocks is an appropriate explanation to the asymmetric rifting of the South China Sea.