As primary producers, phytoplankton play an important role in the material cycle and energy flow of marine ecosystems. Changes in the phytoplankton community can effectively reflect changes in climate and marine ecological environment and affect the bait availability of fishery organisms. During extreme climate events, such as El Ni?o, the phytoplankton community displayed an obvious interannual variation trend, which affected the fishery yield by affecting the food chain. Based on the phytoplankton and water environment survey results of 12 voyages on the Miaodao Archipelago waters in May (dry season) and August (wet season) from 2015 to 2020, the interannual variation of phytoplankton community and its relationship to environmental factors according to climate change were evaluated based on precipitation data and three El Ni?o events during the survey period. A total of 109 species belonging to 45 genera and four phyla were identified. Bacillariophyta accounted for 85.32% of the total number of algae, followed by Dinoflagellates (11.93%). During the dry season, the abundance of diatom was always higher than 90%, and Paralia sulcata was identified as the dominant species. In the wet season, the abundance proportion of dinoflagellates gradually increased from 0.5% to 58.7%, and Chaetoceros nipponicus and Tripos muelleri were the dominant species. The main environmental factors affecting the phytoplankton community were water temperature, precipitation, and SiO₃ ^2–Si levels. The dominant diatom species were mainly regulated by the levels of NO₃ ^– -N, SiO₃ ^2–Si, and DIN related to precipitation, while the main influencing factor of dinoflagellate abundance was the water temperature. A significant negative correlation was found between the abundance of Paralia sulcata and SiO₃ ^2–-Si concentration (P＜0.05). Further, the abundance of Chaetoceros nipponicus showed a significant positive correlation with precipitation levels in the first two months (P＜0.05). The similarity of the phytoplankton community structure under extreme drought was significantly lower than that during other voyages. During the El Ni?o influence period of 2018/2019 and 2019/2020, the phytoplankton abundance in the dry and wet periods of 2019–2020 decreased by 93.2% compared with that of 2015–2018. The changes in the number and abundance of the phytoplankton species occurred in the next year of El Nino, which may be related to the climate changes in the coastal waters north of the Yangtze River in China, such as the reduced rainfall in the subsequent year owing to the El Ni?o effect. Extreme climate events became one of the important driving factors for the interannual variation of phytoplankton communities. Due to climate change, the interannual increase in water temperature, decrease in precipitation, and decrease in nutrient level led to noticeable changes in the phytoplankton community, such as a decrease in phytoplankton abundance and the succession of the phytoplankton community. These results serve as a reference for the rational exploitation and utilization of fishery resources and planning of fishery resource expansion and conservation.