Mantle convection could have a significant effect on basin evolution; however, research quantifying this relationship is controversial. To understand the formation mechanism and evolution of the Cenozoic rift basins in eastern China, we applied the back-stripping technique and strain rate inversion modeling to 119 wells from Sangjiang Basin, Bohai Bay Basin, North Yellow Sea Basin, South Yellow Sea Basin, East China Sea Shelf Basin, and four basins within the northern South China Sea margin. The modeled results can be used to reconstruct the tectonic subsidence history and further assess the potential subsidence mechanisms of eastern China. Residual subsidence is defined as the difference between the theoretical and observed tectonic subsidences. Our results show that the residual subsidence since 20Ma in eastern China generally increases from ∼100 to 300m in terrestrial areas to ∼1.2–1.8km onthe continental shelf. Our observed residual subsidence is generally consistent with the present-day dynamic topography that is predicted from mantle flow models, and it is associated with a stagnant slab within the mantle that has been observed by seismic tomography. The migration pathway of the residual subsidence since 20Ma is consistent with the movement direction of the Pacific and Philippine plates. Therefore, we suggest that the residual subsidence might be a dynamic subsidence induced by a negative buoyancy of the sinking slab in the deep mantle beneath eastern China.