The South China Sea continental margin in the Qiongdongnan Basin (QDNB) area has incrementally prograded since 10.5 Ma generating a margin sediment prism more than 4km‐thick and 150–200 km wide above the well‐dated T40 stratigraphic surface. Core and well log data, as well as clinoform morphology and growth patterns along 28 2D seismic reflection lines, illustrate the evolving architecture and margin morphology; through five main seismic‐stratigraphic surfaces (T40, T30, T27, T20 and T0) frame 15 clinothems in the southwest that reduce over some 200 km to 8 clinoforms in the northeast. The overall margin geometry shows a remarkable change from sigmoidal, strongly progradational and aggradational in the west to weakly progradational in the east. Vertical sediment accumulation rate increased significantly across the entire margin after 2.4 Ma, with a marked increase in mud content in the succession. Furthermore, an estimate of sediment flux across successive clinoforms on each of the three selected seismic cross sections indicate an overall decrease in sediment discharge west to east, away from the Red River depocenter, as well as a decrease in the percentage of total discharge crossing the shelf break in this same direction. The QDNB Late Cenozoic continental margin growth, with its overall increased sediment flux, responded to the climate‐induced, gradual cooling and falling global sea level during this icehouse period.