In summer, large areas of low dissolved oxygen or hypoxia are prone to occur in the bottom waters of Changjiang (Yangtze River) Estuary. The zooplankton community (＞160 μm) in hypoxic area (DO＜2 mg/L), low dissolved oxygen area (2 mg/L＜DO＜3 mg/L) and normal area (DO＞3 mg/L) of the Changjiang Estuary in summer of 2016 and 2017 were compared. The results showed that the abundance and biomass of zooplankton in hypoxic area were significantly higher than those in the low dissolved oxygen area and normal area in 2016. The abundance of small mediumsized copepods and gelatinous zooplankton in hypoxic area and the low dissolved oxygen area were all higher than those in the normal area. It was dominated by filterfeeding of the class Thaliacea and Appendiculata in the summer of 2016 when the degree of hypxia was more serious, but in the summer of 2017, it was dominated by carnivorous Chaetognaths of the class Sagitta.