The Neogene Yinggehai-Huangliu Formation in the Qiongdongnan basin consists of very thick marine deposits. Many cycles of sea-level changes have occurred in this epoch. The sea-level changes were related to sequences and bioevents. Based on quantitative studies of the abundance and diversity of foraminifers from the Ya-A-2 well and oxygen and carbon isotopic records of planktonic foraminiferal tests from the Ya-A-1 well, the relative sea level change curve has been constructed in the Yinggehai-Huanglui Formation. In addition, the paper analyzes the migration of the onlap point in main seismic data and reconstructs the paleodepth of the sea water according to the slope-basin depositional system in the Qiongdongnan basin. Nine sequences have been recognized based on seismic data. Sequence chronostratigraphy has been established in the light of newly-revised geomagnetic polarity time scale for the Cenozoic, new late Neogene time scale and Cenozoic geologic time scale. The ages of nine depositional sequence boundaries have been determined again.