Six field surveys were conducted in the Changjiang Estuary for studying the relationship between the zooplankton abundance and its environment in May and August from 2004 to 2006. It was evidenced that the abundance was higher in August, in the North Branch and in the brackish waters, respectively compared with the situation in May, in the South Branch and in the Estuary. In general, the offshore abundance was higher than littoral′s in May, but it was completely opposite in August. The number of zooplankton species in the Changjiang Estuary and their distributions are complicated. It is due to the fluctuation in the quantity of runoff, especially Changjiang Dilute Waters (CDW). And also, the variation in salinity has had a great influence on the zooplankton species composition. In the South Branch, Sinocalanus sinensis and Schmackeria poplesia are main dominant species in May and August, respectively. There are many dominant dspecies both in the North Branch and in the littoral, such as Labidocera euchaeta, as well as Paracalanus parvus; Paracalanus aculeatus, Centropages dorsispinatus and Acartia pacifica. While offshore, Calanus sinicus is main dominant species, and then Muggiaea atlantica and Sagitta enflata.