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• The continental margin of SCS evolved through differential stretching and paleogeography. • Flexural interpolation of sparsely distributed data can provide excellent subsidence evolution. • Coevality of uplift in a basin make the sediment rates inconsistent with subsidence. • Stress directions, paleogeography, and differential crust relocate the sediments geometry. • Accumulation of thick deposits insight into the highly stretched and mechanically weak zones. The South China Sea (SCS) is the largest marginal sea on the SE Asian continental margin, located at the junction of the Pacific, Indo-Australia and Eurasian plates, and has undergone the joint effect of the Tethys and Pacific tectonic domains. Currently, the SCS remains debatable for its evolution and origin. However, its northern margin preserves the Cenozoic tectonic and subsidence history, which allow us to restore the past continental margin (0–33.7 Ma), to estimate subsidence, thickness and sediment accumulation correlated with regional tectonics. This paper has employed a 2D flexural backstripping technique and spatio-temporal variations by enhancing the seismic profiles with flexurally interpolated modelled sections. According to our findings, the transition was mainly controlled by three structural stages. (1) Early-Late Oligocene: records the highest subsidence due to the initiation of seafloor spreading, isostatic response of continental breakup, associated uplifts therein, and retreat of the Pacific Plate. (2) Early-Middle Miocene: mature spreading attributed to a slow phase of subsidence during the Early Miocene and a rapid increase of subsidence associated with the closure of the SCS in the Middle Miocene. (3) Thermal subsidence: sediments shifted since the Late Miocene towards mechanically weak and stretched regions (central-southern and eastern) which were triggered by a gravitational pull force. A fault system and differential stretched crust relocated sediment to the regional stress directions of the Pacific Plate. [ABSTRACT FROM AUTHOR]