Abstract: This article applies the theory and methods of biological integrity to the coastal waters of the Beibu Gulf, constructs the zooplankton biological integrity index (Z-IBI), and uses this index to evaluate the ecological health of the coastal waters of the Beibu Gulf from 2016 to 2020. The study aims to explore the applicability of Z-IBI in the Beibu Gulf waters and analyze the ecological health status of the waters. The results showed that among the three water periods (wet season, dry season, and normal season) in the Beibu Gulf, the ecological health evaluation results were the best during the wet season, with a Z-IBI score of 3.398; The dry season comes second, with a score of 3.045; The performance was the worst during the normal season, with a score of 3.011. Most waters near the coast of the Beibu Gulf are in a healthy state, but the ecological conditions of Qinzhou bay and Fangcheng port (bay) urgently need to be improved. Z-IBI is positively correlated with water quality categories in all three water periods, indicating its applicability and wide potential for application in ecological health assessment.