Mantle induced dynamic topography may have a significant effect on the accomodation space in sedimentary basins, especially close to “slab burial grounds”, but its magnitude and relevance is controversial. We use five Cenozoic stratigraphic sections and 56 wells from the northern South China Sea margin to assess all mechanisms contributing to Late Tertiary tectonic subsidence in this area and to ground-truth the dynamic topography output of a mantle convection model. The computed dynamic topography decreases on average by about 300 m from 20 Ma to the present in the northern South China Sea area. Post-rift anomalous subsidence is computed as the discrepancy between observed and predicted post-rift subsidence based on modeling exponential thermal cooling following earlier lithospheric thinning events. In shallow water areas its magnitude is similar to that predicted by the mantle convection model, confirming that the change in dynamic topography through time since 20 Ma agrees well with subsidence unaccounted for by a conventional rift model. However, this mechanism does not explain the rapid increase of anomalous subsidence towards the deep water areas in the Qiongdongnan and Pearl River Mouth basins. In the deep water (>500 m) part of the Qiongdongnan and Pearl River Mouth basins, post-rift anomalous subsidence ranges from 900 to 1200 m, whereas in the continental shelf area of the basins it ranges from 700 to 300 m and decreases landwards, to less than 250 m in the Beibuwan Basin. This rapid subsidence event, preceded by minor uplift, is interpreted as a thermal cooling episode induced by a late magmatic event. In the Yinggehai Basin anomalous subsidence during the post-rift stage is about 300–500 m in the northwestern part of the basin, substantially less than that in the middle and southeastern parts, where it ranges from 900 to 1200 m. The distinct subsidence anomaly in the Yinggehai Basin may originate from a combination of the dextral movement of marginal faults since the Late Miocene and the effect of dynamic topography.