Abstract: In recent decades, due to climate change and human activities, ecological disasters occurred frequently in Chinas offshore estuarine waters, especially in Changjiang Estuary and adjacent waters, where the health of marine ecosystems and their service functions have been affected. Based on the IPCC theoretical framework of comprehensive risk of climate change and related literature, this paper firstly formed a comprehensive risk of climate change assessment index system for estuarine phytoplankton ecosystems, and combined with IPCC CMIP5 earth system model data, calculated and analyzed the future (2030—2039, 2050—2099 and 2090—2099) hazard, exposure, vulnerability and risk of phytoplankton ecosystems under different climate scenarios (RCP 2.6, 4.5, 8.5). Results show that under RCP 2.6, 4.5 and 8.5 scenarios, the hazard of disaster-causing factors will increase significantly by the middle of this century. Under RCP 4.5 and 8.5 scenarios, it will increase significantly by the end of 21st century and it will be the most significant with RCP 8.5. While under RCP 2.6 scenario it will decrease and high exposure areas will mainly located in areas near Changjiang Estuary with little change in different years. High exposure areas under RCP 4.5 and 8.5 scenarios are significantly larger than those under RCP 2.6 scenario, especially the latter it will expand to its adjacent waters by the end of this century. Vulnerability generally shows a distribution characteristic of high near the shore and low in the offshore with little fluctuations. Under RCP 2.6, 4.5 and 8.5 scenarios, comprehensive risk shows a strengthened trend of high near shore and low offshore with the most seriousness under RCP 8.5 scenario to its maximum at the end of this century.