Assessing fishery resources is crucial for sustainable marine ecosystem management and the operation of fisheries. This study integrates trawl surveys, environmental DNA (eDNA) analysis, and scientific echo sounder techniques to analyze the fishery resource distribution of and seasonal variations in the East China Sea. Surveys were conducted in April, July, August, and November 2022, utilizing bottom trawl sampling, eDNA metabarcoding, and acoustic data collection. The results revealed temporal differences in species composition, with crustaceans dominating in terms of abundance and fish species in biomass. The integration of eDNA analysis provided broader species detection, including cryptic and pelagic species, while acoustic techniques enabled large-scale resource assessment. However, discrepancies between methods highlighted the need for methodological refinement. Dominant species exhibited seasonal variation, with Portunus trituberculatus prevailing in spring (April), Trachurus japonicus and Scomber japonicus in summer (July–August), and Pampus argenteus in late autumn (November). A comparative analysis revealed that eDNA is sensitive to pelagic and cryptic species, trawl surveys effectively detect demersal fish, and acoustics allow for broad-scale biomass estimation, highlighting the complementary value of method integration.