Determining accurate chronologies of sand cay formation is key to understanding their temporal dynamics and stability and their potential as paleo-archives. We reconstruct the growth of a sand cay strongly influenced by frequent tropical cyclones in the South China Sea. AMS 14C and U/Th dating of coral, soft coral spicules, mollusk, and benthic foraminifera revealed substantially different ages among calcareous components within layers. Relatively small benthic foraminifera, including Amphistegina sp., Rotalia calcarinoides, and Calcarina hispida, yielded abnormally old ages, suggesting a disparity of centuries to millennia between the organism death and final deposition. U/Th ages derived from Acropora branches with eroded surfaces exhibited variable but older ages, while AMS 14C ages from gastropod and large benthic foraminifera exhibited younger ages within the same layers. Taphonomically pristine Acropora branches commonly recorded in ‘cyclone-deposit’ layers were consistently the youngest component of all radiometric ages, and align with paleo-typhoon records throughout the Little Ice Age. Age distribution pattern of the dated coral fragments also provides a detailed record of the island formation history.