Abstract: The Miocene Meishan Formation in the Qiongdongnan Basin in the northern continental shelf of the South China Sea lacks direct fossil evidence for understanding the ancient vegetation and climate conditions in the basin due to the scarcity of spores and pollen fossils. The Miocene biostratigraphy, vegetation, and climate changes were documented from 114 fossiliferous samples from Well ST-A. Results show that the calcareous nannofossil boundaries of the Sanya Formation (Early Miocene) / Meishan Formation (Middle Miocene) / Huangliu Formation (Late Miocene) are at 2780 m and 2300 m in depth, respectively. Miocene vegetation in the study area was tropical and subtropical evergreen broad-leaved forest, and mixed forest of evergreen broad-leaved and deciduous broad-leaved. The presence of coniferous forest restricted to the uplands shown in the Sanya Formation reflects warmer and wetter climate in Early Miocene than that of the late Oligocene in the Lingshui Formation. The expansion of the evergreen broad-leaved forest and deciduous broad-leaved forest, accompanied by the contraction of the coniferous forest during early and middle stage of the middle Miocene (the bottom and middle section of Meishan Formation), suggested increases in temperature and humidity, which is indicative of the Middle Miocene Climate Optimum (MMCO). The climate conditions in late Miocene (the top of Meishan Formation and Huangliu Formation) turned to be cold, characterizing of the flourish of coniferous forest again. Meishan Formation witnessed the climate variability of warm and cold during the middle Miocene.