Based on quarterly bottom trawl survey data from 2018 to 2019, we analyzed the dynamic changes in fish community structure and their relationship with environmental factors in the survey area using ecological indicators, such as resource density, relative importance index, and diversity index. Results showed that there are 84 fish species in the survey area, belonging to two classes, 14 orders, 39 families, and 69 genera. There were seven dominant species, including Harpadon nehereus, Trichiurus japonicas, Pennahia argentata, Setipinna tenuifilis, Benthosema pterotum, Stolephorus commersonnii, and Amblychaeturichthys hexanema, whose composition has changed dramatically. The highest biomass index value was in summer, at 3.25×10³ kg/km² . The highest abundance index value was in autumn, which was 6.64×10⁵ ind/km² . The highest diversity index values of H′ and J′ were in winter, at 1.92 and 0.71. The distribution of T. japonicus and B. pterotum is positively correlated with depth and salinity. The distribution of P. argentata is strongly positively correlated with temperature and negatively correlated with pH. S. commersonnii, S. tenuifilis, and H. nehereus have a low preference for environmental factors. By exploring the spatial and temporal changes of fish community structure in the Oujiang River Estuary, the results of this study provide scientific evidence for protecting fishery resources and improving the quality and function of fishery environments in the estuary area.