Abstract: The Qiongdongnan Basin is located at the western end of the northern continental margin of the South China Sea. Compared to the active magmatism observed in the northeastern margin, its deep magmatic activity is relatively subdued, resulting in a lack of evidence for high-velocity anomalies typically associated with lower crustal underplating. To investigate the intensity and extent of deep mantle upwelling beneath the Qiongdongnan Basin under weak magmatic conditions, we employed a joint gravity-seismic inversion method to construct the crustal density structure and analyze the origin of high-density anomalies. Results reveal the presence of high-density anomalous bodies in the lower crust (below 20 km depth) and upper mantle beneath the central part of the basin, with densities ranging from 2.90–2.96 g/cm³ to 3.34–3.40 g/cm³, respectively. Correspondingly, the crust in this region exhibits extreme thinning, decreasing from ～26 km at the continental margin to ＜10 km in the central area, with the thinnest section measuring only ～5 km. Additionally, the whole-crustal stretching factor exceeds 3.0, indicating hyper-extensional thinning characteristics. Integrated with previous studies, we infer that the Qiongdongnan Basin underwent widespread crustal hyper-extension during the rifting phase, triggering extensive mantle upwelling and lower crustal underplating, which contributed to the formation of high-density anomalies in the lower crust. Due to their relatively small scale and weak magmatic signature, these features pose significant challenges for seismic detection. Therefore, the gravity-seismic joint inversion method proves crucial for identifying deep mantle upwelling and lower crustal underplating in low-magma-activity settings, providing key insights into the formation and evolution mechanisms of the South China Sea as well as its magmatic processes.