The coral reef fish community in the Beijiao Atoll of the Xisha Islands has undergone significant changes in fishery resources due to human disturbances and climate change. This study conducted a survey of fish resources at the Beijiao Atoll of the Xisha Islands, integrating historical data to analyze the species composition and changes in fish communities. As of April 2023, a total of 270 fish species were identified in the Beijiao Atoll, belonging to 12 orders, 49 families, and 121 genera, with the order Perciformes having the highest number of species at 212, accounting for 78.52% of the total species. The community structure of coral reef fish in the Beijiao Atoll has undergone significant changes compared to the historical data. The number of large fish and carnivorous fish species has notably decreased, with proportions not collected being 43% and 27%, respectively, which were the highest values among different size and trophic groups. Moreover, the similarity with the historical data was less than 0.25, indicating extreme dissimilarity. The average taxonomic distinctness (Delta+) and the variation taxonomic distinctness (Lambda+) of fish composition have significantly decreased from 56.72 and 163.8 for 1998-2003 to 54.57 and 107.6 in 2023, respectively. Additionally, the proportions of orders, families, and genera to species numbers have significantly decreased by 48.21%, 34.67%, and 15.45%, respectively. Furthermore, the similarities of fish species composition in terms of orders, families, genera, and species between different periods were 0.50, 0.37, 0.23, and 0.10, indicating dissimilarity and extreme dissimilarity. The results indicate an evolutionary trend of the coral reef fish community in the Beijiao Atoll towards herbivory, small-sized fish dominance, and simplicity. This study contributes to a better understanding and prediction of the species composition and evolutionary trends of coral reef fish in the Beijiao Atoll, which is crucial for ensuring the health and recovery of coral reef ecosystems.