Fluvial-marine transitional facies, including braided river delta and estuary-tide flat, were mainly developed in sags of Qiongdongnan Basin，northern South China Sea. Under the guide of high-resolution sequence stratigraphy theory，the Members 2 and 3 of Paleogene Lingshui Formation were divided into 2 long-term base-level cycles and 10 mid-term base-level cycles. Sedimentary characteristics and evolution of the Members 2 and 3 of Lingshui Formation were discussed under isochronous stratigraphic framework. Braided river delta, with unique stratification structures, rich mud lamina and abundant trace fossils, was mainly developed in the Member 3 of Lingshui Formation, and its evolutionary process could be divided into 3 stages: the early period dominated by fluvial activities(S1-S4)，the middle period affected by fluvial and tidal activities(S5-S6), and the late period dominated by tidal activities(S7-S8). During the depositional period of Member 2 of Lingshui Formation(S9-S10)，a comprehensive transgression happened in study area, resulted in more complicated sedimentary characteristics and process with more unique biogenic structures, which was interpreted as estuary-tide flat. According to this research，the relative sea level change was the controlling factor of base-level cycle and sedimentary evolution in Qiongdongnan Basin.