AbstractA number of major controversies exist in the South China Sea, including the timing and pattern of seafloor spreading, the anomalous alternating strike‐slip movement on the Red River Fault, the existence of anomalous post‐rift subsidence and how major submarine canyons have developed. The Qiongdongnan Basin is located in the intersection of the northern South China Sea margin and the strike‐slip Red River fault zone. Analysing the subsidence of the Qiongdongnan Basin is critical in understanding these controversies. The basin‐wide unloaded tectonic subsidence is computed through 1D backstripping constrained by the reconstruction of palaeo‐water depths and the interpretation of dense seismic profiles and wells. Results show that discrete subsidence sags began to form in the central depression during the middle and late Eocene (45–31.5 Ma). Subsequently in the Oligocene (31.5–23 Ma), more faults with intense activity formed, leading to rapid extension with high subsidence (40–90 m Myr−1). This extension is also inferred to be affected by the sinistral movement of the offshore Red River Fault as new subsidence sags progressively formed adjacent to this structure. Evidence from faults, subsidence, magmatic intrusions and strata erosion suggests that the breakup unconformity formed at ca. 23 Ma, coeval with the initial seafloor spreading in the southwestern subbasin of the South China Sea, demonstrating that the breakup unconformity in the Qiongdongnan Basin is younger than that observed in the Pearl River Mouth Basin (ca. 32–28 Ma) and Taiwan region (ca. 39–33 Ma), which implies that the seafloor spreading in the South China Sea began diachronously from east to west. The post‐rift subsidence was extremely slow during the early and middle Miocene (16 m Myr−1, 23–11.6 Ma), probably caused by the transient dynamic support induced by mantle convection during seafloor spreading. Subsequently, rapid post‐rift subsidence occurred during the late Miocene (144 m Myr−1, 11.6–5.5 Ma) possibly as the dynamic support disappeared. The post‐rift subsidence slowed again from the Pliocene to the Quaternary (24 m Myr−1, 5.5–0 Ma), but a subsidence centre formed in the west with the maximum subsidence of ca. 450 m, which coincided with a basin with the sediment thickness exceeding 5500 m and is inferred to be caused by sediment‐induced ductile crust flow. Anomalous post‐rift subsidence in the Qiongdongnan Basin increased from ca. 300 m in the northwest to ca. 1200 m in the southeast, and the post‐rift vertical movement of the basement was probably the most important factor to facilitate the development of the central submarine canyon.