We analyzed two recently acquired multichannel seismic profiles across the Dangerous Grounds and the Reed Bank area in the South China Sea. Reconstruction of the tectonic subsidence shows that the southern continental margin can be divided into three stages with variable subsidence rate. A delay of tectonic subsidence existed in both areas after a break-up, which was likely related to the major mantle convection during seafloor spreading, that was triggered by the secondary mantle convection below the continental margin, in addition to the variation in lithospheric thickness. Meanwhile, the stage with delayed subsidence rate differed along strikes. In the Reed Bank area, this stage is between 32–23.8 Ma, while in the Dangerous Grounds, it was much later (between 19–15.5 Ma). We believe the propagated rifting in the South China Sea dominated the changes of this delayed subsidence rate stage.