Abstract: The saltwater intrusion is a major influencing factor on the diversity index, dominance index, evenness index and other indicators of plankton in Changjiang River Estuary. To study the impact of saltwater intrusion on plankton, an analysis was conducted based on the salinity data from representative hydrological stations in Changjiang River Estuary from 2020 to 2022 and the quarterly collected plankton sample data. The results showed that during the study period, there were 88 species of zooplankton and 367 species of phytoplankton in Changjiang River Estuary, with copepoda being the main group of zooplankton and diatoms being the main group of phytoplankton. From the perspective of spatio-temporal changes, the diversity of plankton was significantly higher in large annual runoff than small annual runoff. The north branch was dominated by salt-tolerant plankton, and the south branch was primarily freshwater communities, while the north channel was mainly halophilic plankton communities. The saltwater intrusion can alter the distribution of plankton, with marine plankton entering the north channel and even further upstream into the south branch as the saline tide advances. Phytoplankton diversity was not only related to absolute salinity, but also significantly positively correlated with the variation range of salinity. The greater the annual variation range of salinity, the relatively fewer species of phytoplankton can survive, the lower the diversity and evenness, the higher the dominance, and the dominant species change to wide-salinity organisms.