The Changjiang (Yangtze River) Estuary has been subject to the double pressure of human activities and natural changes for a long time. As a result, the change of environmental factors may lead to a great alteration of phytoplankton community composition in this area. To explore the composition and variation of phytoplankton community in the Changjiang Estuary and compared with historical data, phytoplankton samples were collected vertically using net trawl method during “LORCE” cruise in August of 2017. Among all the samples collected, 7 phyla, 86 genera, and 205 species were identified, their total abundance was 1.47×105 cells/L. The results showed that diatoms and dinoflagellates accounted for 95.8% and 1.2% of the total phytoplankton abundance, respectively. Warmwater species, including Pseudonitzschia delicatissima (56.35×103 cells/L), Trichodesmium thiebautii (3.30×103 cells/L), Pseudosolenia calcaravis (3.05×103 cells/L), Chaetoceros lorenzianus (2.64×103 cells/L), Proboscia alata (1.89×103 cells/L) and Coscinodiscus gigas (1.71×103 cells/L), were dominant in the phytoplankton community. Their total abundance was 68.94×103 cells/L, which accounted for 47.00% of the total abundance of netcollected phytoplankton. High abundances of these warmwater species were observed near the front formed by the convergence of the Changjiang Diluted Water and Taiwan Warm Current. Spearman’s rank correlation showed that C. lorenzianus and P. calcaravis were negatively correlated with phosphorus, C. gigas were positively correlated with the concentrations of dissolved inorganic nitrogen, and P. calcaravis was positively correlated with salinity, C. lorenzianus and C. gigas were negatively correlated with salinity. Compared with the summer dominant phytoplankton species during the past 30 years, it was found that warmwater species of phytoplankton in the Changjiang Estuary increased significantly and their distribution area expanded northward. It was speculated that this phenomenon was highly associated with sea temperature elevation and the enhancement of warm current.