Carbonate strata are a vital and favorable reservoir for global oil and gas exploration, and carbonate sedimentary systems record ancient oceanic and paleoclimatic conditions, including paleoenvironmental variations throughout geologic periods. Carbonate platforms are widely distributed among the Xisha Islands in the South China Sea and contain large amounts of oil and gas resources. Biogenic reefs are the dominant parts of the carbonate platforms in the Xisha Islands; however, research on the factors that control and affect biogenic reef development is lacking. In this study, a core from well XK-1, which is located on Yongxing Island in the Xisha Islands, a sedimentary noise model, and time-series analyses were used to determine the effects of sea-level fluctuations from 5.3 Ma to present. The results show that coral reefs in the Xisha Islands are sensitive to eustatic fluctuations and that a decrease in sea level essentially corresponds to an increase in sedimentation rate. Indexes of the East Asian monsoon and other environmental indexes show that the Pleistocene and Holocene were suitable for coral growth; however, the trends shown by these indexes and the sea-level variation indicate that the future growth of coral reefs will be at a disadvantage. Research on the controlling factors of biogenic reefs is of significance for understanding reef growth, performing global reef comparisons, and encouraging the future protection of coral reefs.