Abstract: In recent years, intensified human activities and climate change have increasingly impacted the community structure of fishery resources in the Yangtze River Estuary. To elucidate the mechanisms underlying changes in fishery community structure, this study analyzed data from spring bottom trawl surveys conducted continuously over two years (2022–2023) in the Yangtze River Estuary. Community structure characteristics, including species composition, dominant species, and zoogeographical patterns, were examined. Canonical correspondence analysis (CCA) and hierarchical clustering were applied to investigate interannual variations and driving factors of fishery communities. Results revealed that fishery assemblages clustered into three groups: nearshore (CJCA), southern (CJSA), and northern (CJNA) regions, dominated respectively by estuarine, warm-water, and cold-water fauna. Compared to 2022, both species abundance and mean individual size significantly decreased in 2023, while no significant differences in mean abundance or size were observed among the three clusters. CCA indicated that the first two axes explained 25.5% of the total variation in species–environment relationships, with axis 1 reflecting latitudinal distribution mainly driven by temperature, and axis 2 representing interannual variability likely associated with fishing pressure and salinity fluctuations. This study demonstrates that the fishery community structure in the Yangtze River Estuary is influenced not only by temperature and salinity but also by variations in fishing intensity.