The Huizhou sag is situated on the continental shelf of the northern continental margin of the South China Sea. In this paper we present a grid of reflection seismic and well data to characterize the basin structure and prominent unconformities. We employ EBM and 2DMOVE softwares to explore the subsidence history and stratigraphic development history of the basin. We found a rapid subsidence period since 15.5 Ma. Moreover, we calculated the stretching factors of the upper crust and the whole crust in the Huizhou sag. The results show the values are 1.10–1.13 and 1.08–1.31, respectively, indicating faulting in Huizhou sag is relatively small. It is noteworthy that the faults map reveals en echelon distribution at the north and south margins of the basin. We suggest en echelon faults here are caused by the subduction of Proto-South China Sea toward NW Borneo block and cease of the South China Sea. Considering the pronounced unconformities, subsidence rates, fault activities and sediment thickness, the Cenozoic tectonic evolution of the basin can be divided into rifting(49–32 Ma), post-rifted(32–15.5 Ma) and rapid subsidence(15.5–0 Ma) stages. Our study will shed new light on the tectonics of SE Asia and petroleum exploration in the South China Sea. The Huizhou sag is situated on the continental shelf of the northern continental margin of the South China Sea. In this paper we present a grid of reflection seismic and well data to characterize the basin structure and prominent unconformities. We employ EBM and 2DMOVE softwares to explore the subsidence history and stratigraphic development history of the basin. We found the rapid factors of the upper crust and the whole crust in the Huizhou sag. The results show the values ​​are 1.10-1.13 and 1.08-1.31, respectively, indicating faulting in Huizhou sag is relatively small. It is noteworthy that the faults map reveals en echelon distribution at the north and south margins of the basin. We suggest en echelon faults here are caused by the subduction of Proto -South China Sea toward NW Borneo block and cease of the South China Sea. Considering the pronounced unconformities, subsidence rates, fault activities and sedim ent thickness, the Cenozoic tectonic evolution of the basin can be divided into rifting (49-32 Ma), post-rifted (32-15.5 Ma) and rapid subsidence (15.5-0 Ma) stages. Our study will shed new light on the tectonics of SE Asia and petroleum exploration in the South China Sea.