<p>The Dangerous Grounds, located in the southern margin of the South China Sea, has experienced three distinct tectonic evolution stages during the Cenozoic: continental rifting, breakup from the South China Block and southward drift, and collision with Borneo, accompanied by a north-to-south shift in its paleogeographic environment. This study utilized a robust dataset comprising 67 seismic reflection profiles, integrated with drilling and dredging data, to reconstruct the sedimentary filling history of the Dangerous Grounds. By correlating sediment budget outcomes with the spatial distribution characteristics of the sediment thickness, we have gained valuable insights into the region’s sedimentary evolution. Our findings reveal a progressive increase in sediment budgets across the three tectonic stages, despite relatively stable sediment budgets during the southward drift stage associated with seafloor spreading. Spatial sediment distribution shows a continued decrease in the east and expansion in the south and west. By integrating the temporal and spatial distribution of depocenters with drilling results and sediment provenance through geochemical analyses, we provide a comprehensive regional perspective on the factors controlling sediment budget trends, including regional tectonic events, monsoon, sea level change, and the river systems associated with paleogeographic environment variations. The sedimentary inputs to the Dangerous Grounds have shifted over time, with Paleocene-Eocene sediments primarily originating from the north. From the Oligocene to the Early Miocene, northern sediment supply progressively declined, while inputs from the southwest, transported through river systems originating in the Indochina and Malay Peninsulas, gradually increased. Since the Mid-Miocene, the collision with Borneo has led to enhanced sediment supply from the south, with sediments predominantly accumulating along slope edges, channel outlets, and within the Nansha Trough.</p>