Abstract: Tectonic subsidence analysis is helpful for understanding the origin and evolution of a basin, which are critical for basin analysis. In order to reveal the characteristics of Cenozoic tectonic evolution of the continental margins of the southwest sub-sea basin, South China Sea, the multi-channel seismic profile lines, NH973-3 and NH973-1+SO27-04 across the continental margins, were selected as research targets. The structures of the continental margins are studied using the methods of back stripping and balanced profile. It is observed that: (1) the structural subsidence curves of the above-mentioned continental margins are characterized by a multiple segment pattern in a reversed “s” shape, with a gentle slope in the initial rifting stage, a steep slope in the strong rifting stage and the end stage. The slope of the curve return to the relatively gentle during the transitional period from fault-depression to subsidence; (2) the tectonic subsidence along the continental margins have certain time delay, probably due to the layered differentiation and the extension of lithosphere and the dextral strike slip movement of the faults on the western margin of the South China Sea. The dextral strike slip movement of the faults on the western margin of the South China Sea might have resulted in the southward migration of the tectonic subsidence centers; (3) The basins on the continental margins were mainly formed in Late Oligocene, as the basins related to extensional strike slip on the northern margin of the South China Sea were formed due to the modification of the dextral strike slip movement of the west margin fault in Late Oligocene, whereas the flexure-extensional complex basins formed on the southern margin of the South China Sea due to the compression and collision in Early Miocene. The research results have provided important scientific background for the exploration and development of hydrocarbon and gas hydrate in the sedimentary basins on both sides of the southwest sub basin of the South China Sea.