Yongle Atoll was the largest atoll in the Xisha Islands of the South China Sea, and it was a coral reef ecosystem with important ecological and economic values. In order to better protect and manage the coral reef fish resources in Yongle Atoll, we analyzed field survey data from artisanal fishery, catches, and underwater video from 2020 to 2022 and combined historical research to explore the changes in fish species composition and community structure in Yongle Atoll over the past 50 years. The results showed that a total of 336 species of fish were found on Yongle Atoll, belonging to 17 orders and 60 families. Among them, Perciformes had the most fish species with 259 species accounting for 77.08% of the total number of species. The number of fish species in the coral reef of Yongle Atoll was exponentially correlated with its corresponding maximum length and significantly decreases with its increase. The fish community structure of Yongle Atoll changed, and the proportion of large carnivorous fish decreased significantly, while the proportion of small-sized and medium-sized fish increased. At the same time, Yongle Atoll has 18 species of fish listed on the IUCN Red List, 15 of which are large fish. The average taxonomic distinctness (Delta+, Δ+) and the variation taxonomic distinctness (Lambda+, Λ+) in 2020–2022 were lower than the historical data, and the number of fish orders, families, and genera in Yongle Atoll has decreased significantly, which indicates that the current coral reef fish species in Yongle Atoll have closer relatives and higher fish species uniformity. In addition, the similarity of fish species in Yongle Atoll was relatively low at various time periods, further proving that the fish community structure has undergone significant variation. In general, due to multiple impacts, such as overfishing, fishing methods, environmental changes, and habitat degradation, the fish species composition of Yongle Atoll may have basically evolved from carnivorous to herbivorous, from large fish to small fish, and from complexity to simplicity, leaving Yongle Atoll in an unstable state. Therefore, we need to strengthen the continuous monitoring of the coral reef ecosystem in Yongle Atoll to achieve the protection and restoration of its ecological environment and fishery resources, as well as sustainable utilization and management.