The fish community structure and its biotic integrity are indispensable for effective fisheries management. The field surveys were conducted in Zhanjiang Bay waters every August from 2008 to 2012 using pair trawls. A total of 103 species were recorded, of which there were 58 species belonging to Perciformes, including 48 families, 17 orders. The catch per hour and numbers per hour ranged from 39.5 kg/h to 75.1 kg/h and from 1.0×10³ ind/h to 1.8×10⁴ ind/h respectively. Following were the community parameters:Sardinella jussieu was the dominant species for five years; the Margalef's species richness index (D) ranged from 3.34 to 5.03 and the Shannon-Wiener diversity index (H') ranged from 3.34 to 5.03. The average annual biomass was about 93.04±26.44 t from 2008 to 2012. The values of F-IBI showed that the fish community structure was disturbed more severely in 2009 and 2010 than in other three years, and the biological integrity was slightly disturbed in the whole five years, whereas the 53.9% decrease of average body mass of fish from 2010 to 2012 compared with that from 2008 to 2009 indicated the overall decreasing tendency of fish size.