Abstract: Plankton plays a unique role in aquatic ecological system. In order to make clear the correlation between community structure of the plankton and the environmental factors of Duliujian river estuary, investigations were made to 8 sampling sites in May and in August of the year 2015. In total 38 species of phytoplankton and 10 species of zooplankton were identified. The average density of phytoplankton in May was 3.32×10⁵/L, and in August was 1.36×10⁶/L. The Average density of zooplankton in May was 64.4 ind/L, and in August was 18.65 ind/L. For the environmental factors: the average DO concentration in May was 12.3 mg/L, and was 6.69 mg/L in August, the average salinity in May was 32.70, and in August was 33.29. Nitrate-N, Nitrite-N and Total Nitrogen level in August was higher than that of in May. In general, Nitrate-N was the major form of nitrogen during the investigation period. More ammonia was transformed to Nitrate-N in August. The CCA analysis showed that: NO₂^- was the major factor influencing the abundance and diversity of the plankton. High DO level was beneficial to Copepods and Chllorophyta algae. High water temperature was harmful to the growth of Copepod and Chllorophyta, but was favorable to Cyanophyta.