The Beibu Gulf is a semi-enclosed gulf located in the northwestern South China Sea and surrounded by the land territories of China and Vietnam. The region has a tropical to subtropical climate. Thousands of fish and shellfish species have been identified in the Beibu Gulf and support some very important fisheries throughout the year in the region. Large scale resource surveys have been conducted over the last few decades to assess fisheries resources in the Beibu Gulf, and a large quantity of biological and environmental data have been collected. Such scientific data are perfect for evaluating changes in the ecosystem and answers questions such as what changes have occurred over the last few decades to the fisheries ecosystem in the Beibu Gulf? In the study, we analyzed data collected in otter trawl surveys in the Beibu Gulf in autumn 1992, 2001 and 2006 to evaluate fish species composition and diversity, dominant species, and their biomasses. The analysis showed that 171 fish species caught in the 1992 autumn survey in the Beibu Gulf Gulf belonged to 77 families and 17 orders, a total of 156 fish species belonging to 71 families and 18 orders were found in the 2001 survey and 157 species belonging to 67 families and 17 orders were identified in 2006. Perciformes had the highest number of fish species, 96 species (accounting for 56.14%) in 1992, 90 species (57.69%) in 2001 and 89 species (56.69%) in 2006. The Pielou evenness index (J') had the same temporal trend as the Shannon-Wiener diversity index (H'). Both indices were the highest in 2001, followed by those in 1992 and 2006. The Margalef richness index (D) reduced from 21.03 in 1992 to 20.74 in 2001 and to 19.61 in 2006. Nonlinear regression models were developed to quantify the temporal trends of biomass of the 6 dominant species (Acropoma japonicum, Trichiurus haumela, Parargyrops edita, Leiognathus bindus, Trachurus japonicas and Upeneus sulphureus) in the Beibu Gulf. The dominant species were found to shift from the high-value fish species to the low-value species, but no significant changes for fish species with high reproduction rates and short life spans. The catch rates increased during the survey period for A. japonicum and L. bindus, decreased for T. haumela and U. sulphureus, and remained similar for P. edita and T. japonicus. This study shows an apparent succession of the dominant species with an overall trend of the K-selection species (such as Lutjanus sanguineus and Carcharhinus menisorrah) being replaced by the r-selection species (such as A. japonicum,Leiognathus, and Apogonichthys). The abundance of fish species with long life span, large size and high trophic levels decreased, while short-lived and small-sized fish species in low trophic levels increased their abundance over the time period covered by the survey. The study provides important evidence of changes occurring in the Beibu Gulf ecosystem.