This article reconstructs the changes of ancient coastline and the evolution process of Qiongzhou Strait in the Beibu Gulf—Leiqiong area since the Cenozoic Era based on borehole data. Results: In the Paleogene, the Beibu Gulf formed a NEE trending disconnected fault basin and filled with fluvial—lacustrine facies deposits. In the late Oligocene, seawater intermittently invaded the ancient Beibu Gulf lake and connected the isolated fault basin. In the early-middle Miocene（23. 3~10. 4 Ma) , the coastline in the northwest of the South China Sea rapidly retreated, and the ancient lake in the Beibu Gulf evolved into the ancient Qiongzhou Strait. In the late Miocene to Pliocene （10. 4~2. 58 Ma) , the coastline continued to retreat, forming a wide ancient Qiongzhou Strait, early Pleistocene regression and volcanic eruptions led to the shrinkage of the ancient Qiongzhou Strait. Frequent climate fluctuations during the late Early Pleistocene to late Pleistocene controlled the continuous transformation of fjords and land. The significant regression during the last glacial maximum directly led to the transformation of the Beibu Gulf-Leiqiong area from sea to land. Since 15 ~ 12 ka BP, the coastline has rapidly retreated; and briefly stopped between 12 and 11 ka BP, the Beibu gulf has once again transitioned from land to sea. Afterwards, the sea level continued to rise, and the Qiongzhou Strait fully opened from west to east at 11 ka BP. By 6 ka BP, the sea level reached about 2 meters above the current sea level, forming the current sea land pattern.Conclusions: The results indicate that the Beibu Gulf - Leizhou Peninsula—Hainan Island area underwent four evolutionary stages in the Cenozoic, including the Paleogene Beibu Gulf ancient lake, the Neogene to early Pleistocene ancient Qiongzhou Strait, the late Early Pleistocene to late Pleistocene fjords, and the Holocene Qiongzhou Strait.