Flood events can significantly affect the physical and biological processes of aquatic ecosystems in a short time, leading to rapid changes in phytoplankton community structure. The Huayanghe Lakes experienced extreme flooding in the summer of 2020, with the water level reaching 16.42 m. In order to understand the effects of flooding on phytoplankton diversity and community structure, eight samples were collected in the Huayanghe Lakes from 2019 to 2020. Water-level disturbance has a significant influence on lake-water quality and phytoplankton community structure. The results showed that the Secchi depth increased from 65.36 to 8.52 cm, while the concentration of total nitrogen (from 0.98 to 0.7 mg/L) and total phosphorus (from 0.04 to 0.031 g/L) decreased. In addition, flooding significantly increased the Shannon–Wiener diversity index, the Pielou index, and the Margalef richness index by an average of 43.5%, 36.7%, and 40.21%, respectively. The phytoplankton community structure in the Huayanghe Lakes changed due to the change of physicochemical environment caused by flood. While in the pre-flood period phytoplankton was composed of large diatoms (e.g., Aulacoseira granulata), cyanobacteria (e.g., Microcystis sp., Anabaena sp., and Aphanizomenon sp.) and other multicellular taxa, the flood period showed an increase in the proportion of chlorophytes and diatoms that quickly adapted to settle in new environments. Pearson correlations and redundancy analyses showed that water level fluctuation was the most significant environmental factor affecting the phytoplankton community between the regular hydrological cycle and flood periods. There are few studies on phytoplankton in the Huayanghe Lakes, and the present study provides basic data on phytoplankton diversity and community structure. In addition, it provides a theoretical basis for controlling water level change in the Yangtze River.