The impact of global climate change has led to an increase in extreme rainfall events, causing fluctuations in terrigenic inputs that significantly affect aquatic communities. Lake Changhu, the third-largest freshwater lake in Hubei Province, plays a crucial role as a reservoir of aquatic germplasm resources in the middle reaches of the Yangtze River. In recent years, the lake has experienced a series of extreme rainfall events. In response to recent extreme rainfall events, a 42-day mesocosm experiment was conducted to understand the effect of terrigenic inputs on various aspects of phytoplankton in Lake Changhu, such as species composition, abundance, biomass, diversity, community turnover rates, resource use efficiency, and stability. The experiment involved the application of different terrigenic treatments, including a control group (CK, using lake water), low terrigenic input (LT), medium terrigenic input (MT), and high terrigenic input (HT). The results showed a noticeable shift in phytoplankton composition from a co-dominated state of Chlorophyta and Cyanobacteria in the CK treatment to a Cyanobacteria-dominated state in the other terrigenic treatments. Furthermore, the terrigenic inputs increased phytoplankton abundance, community turnover rates, diversity, and resistance. Comparatively, the diversity index of phytoplankton increased by 82.61%, 73.83%, and 70.41% in the LT, MT, and HT treatments, respectively, in contrast to the CK treatment. However, phytoplankton abundance decreased by 6.99%, 15.55%, and 14.76% in the LT, MT, and HT treatments. Additionally, the resource use efficiency decreased by 1.94%, 5.16%, and 14.19% in the LT, MT, and HT treatments, respectively, compared to the CK treatment. These findings provide valuable insights into monitoring and managing the water ecology in Lake Changhu, offering a scientific basis for implementing effective management strategies.