Driven by sea-floor spreading, the tectonic evolution of a marginal basin could be divided into three stages, namely the pre-spreading, spreading and post-spreading stages. Most of the thick deposits developed in the Central basin of the South China Sea, especially the thickest in the eastern Sub-basin was deposited in the post-spreading stage. Various factors were active in different parts of the eastern Sub-basin, resulting in a great variety of post-spreading stratigraphic features. A great amount of information about the formation and evolution of the South China Sea was preserved in the thick sediments. Therefore, it is important to study the stratigraphic features in the eastern Sub-basin formed during the post-spreading stage. According to the age data from some ODP and IODP drilling holes, the synthetic seismic records passing through the wells were calibrated and then the sequence stratigraphy of the region was established and dated. Upon the basis, we discussed in this paper the characteristics of the strata and related factors. The result shows that deposition of the sediments with stable thickness was mainly caused by stable basement subsidence with substantial terrigenous sediments input from the north, and the micro-plate subducting toward Manila trench was the main influence factor which gave rise to the characters of the strata in different age in the east. The sediments containing certain amount of volcanic debris was deposited in the west and middle part owing to the frequent magmatic activities. And in the south of the basin, turbidite sediment waves occurred due to the control of slope environment.