This study relies on analyses of the top layer of the material extracted from Well Chenke-2, which is part of a coral reef drilling program in the south-east of Chenhang Island, Xisha Islands. The age of the material at the bottom of the borehole was determined by high-precision uranium dating technology. Five coral samples were selected for the U-Th dating. The five groups of data can be clearly dated to the Holocene or to the Pleistocene. The Holocene part includes samples CK2-15, CK2-16, and CK2-17. Their age was determined as 7 914 ± 67, 7 552 ± 73, and 7 584 ± 55 years, respectively. The Pleistocene part includes samples CK2-18 and CK2-19. Their age was determined as 112 700 ± 700 and 128 100 ± 1 000 years, respectively. Furthermore, a MAT-253 isotope mass content of δ13C, δ18O, and strontium in 21 whole rock samples extracted in the depth interval 0-21 m. Based on the contents of these three elements, the interval can be divided into two parts. The content of δ13C, δ18O, and strontium in the depth interval 0-16 m is higher, with average values of 0.647‰, -3.392‰, and 0.843%, respectively, than that in the depth interval 17-21 m, with average values of -3.185‰, -7.994‰, and 0.174%, respectively. On the basis of the U-Th age, and considering that the contents of δ13C, δ18O, and strontium decrease evidently between 16 and 17 m, it can be concluded that the boundary between the Holocene and the Pleistocene corals is located at a depth between 16 and17 m in Well Chenke-2, and that the age of the corals determined by uranium dating in the upper part of the boundary represents the initiation time of the Holocene reefs. Therefore, it is concluded that the Holocene coral reefs in Chenhang Island started to develop 7 900 years ago, basically simultaneously with most of the Holocene reefs in the Indo-West Pacific, Central Pacific, and Caribbean. The Holocene reefs are 16.7 m thick, and are in unconformity with the late Pleistocene coral reefs (aged 110 ka). Considering the relative stability of the Neotectonic activities in the study area, as well as the fact that the reef flat of the modern coral reefs in the South China Sea is basically located at the low tide height, and that the borehole of Well Chenke-2 is located approximately 2.9 m above the modern reef flat, it is speculated that the top of Well Chenke-2 was originally located about 13.8 m below the low tide level of the modern sea. In other words, the sea level at Xisha Islands 7 900 years ago was about 13.8 m below the modern sea level. This result provides new information for understanding the development history of the Holocene coral reefs in the South China Sea and the sea level changes in the area.