Abstract: Based on the zooplankton survey data in the waters adjacent to the Yangtze River Estuary in the summer and winter seasons of 2020, this study analyzed the species composition, dominant species and community structure of zooplankton in the waters adjacent to the Yangtze River Estuary using DNA metabarcoding and morphological methods to understand the composition of the zooplankton community in this area and its changes. The results showed that 101 species of zooplankton were found in the summer and winter by artificial morphology, and 275 species of zooplankton were found by DNA metabarcoding; the average biomass of zooplankton in the summer and winter was 1 357.5 mg/m³ and 88.1 mg/m³, respectively. The biomass is generally higher inshore than offshore, with a decreasing trend from inshore to offshore. In the summer and winter , the average Shannon diversity index (H') were 1.96 and 1.85, the Margalef’s species richness diversity (D) were 0.39 and 0.40, and Pielou’s evenness index (J) were 0.59 and 0.61, respectively. Community diversity indices were all slightly lower, and zooplankton community diversity was at an average level. The zooplankton biomass in this area showed an increasing trend compared to previous studies, but the composition of dominant species was more stable.