Abstract: The Xisha Trough Basin is a Cenozoic rift basin located in a continental-oceanic transitional zone on the northern slope of the South China Sea(SCS), which separates the Xisha Block from the northern South China Sea continental shelf. In this paper, upon the basis of regional seismic stratigraphic correlation, we divided the Cenozoic of the Trough Basin into nine stratigraphic units. Seismic correlation and seismic facies analysis were carried out to restore the stratigraphic framework and paleo-geomorphology during deposition, and finally we discussed the sedimentary environment evolution process of the Trough Basin. The results show that, during the time from Paleocene to Eocene, the Xisha Trough area was dominated by rivers and lakes. From Oligocene to early Miocene, it became a strait, which separated the land from the northern SCS continental shelf, and connected the Qiongdongnan Basin on one end and the Northwest subbasin on the other. The sedimentary environment gradually changed from shallow water to deep water. Since middle Miocene, the Xisha Trough Basin has become a trough on continental slope. The Central Canyon was formed in the Miocene and became a pathway for turbidity currents under a bathyal-abyssal environment.