Fish is the crucial component of the new approach to diagnose and recover the degraded coral reef. In order to enhance our understanding of long-term variation of species composition and diversity of coral reef fish in the South China Sea and its responses to environmental changes and human activities, using specimens of fish collected by hand fishing and gill net in the lagoon of Meiji Reef in the South China Sea from 1998 to 2018, the long-term variation in species composition, dominant species, diversity of fish were studied. Results showed that compared with 1998—1999, the species composition and dominant species changed significantly from 2012 to 2018. Some species with ecological function, such as fish belonging to Scaridae, Acanthuridae and Chaetodontidae, disappeared or decreased significantly. The species richness of diminant fish decreased, but their dominant degree increased significantly. The relative dominance of first dominant species and the average dominance of all dominant species increased significantly. The number of fish species per unit fishing effort and per sample size decreased significantly. The increase of hand line fishing effort had a significant influence on the increase of corresponding diversity indexes, while the increase of gill net fishing effort had no obvious influence on the increase of corresponding diversity indexes. The gill net sampling method was more robust to assess the diversity indexes of fish in the lagoon of Meiji Reef than the hand line sampling method. Based on fish assemblages collected by gill net, compared with 1999, the species diversity of fish during 2016—2018 in the lagoon of Meiji Reef reduced significantly. It was concluded that the fishing and decrease of ecosystem capacity caused by the decrease of available habitat area of Meiji Reef was the main reason for the decrease of fish species or abundance and diversity. To promote the recovery and protection of fish on the Meiji Reef, it is recommended to take timely measures to protect their resources and improve habitat quality.