Deep lakes are critical for freshwater storage, yet they are struggling against major ecological issues from climate change and nutrient pollution. A comprehensive understanding of internal feedback mechanisms is crucial for regulating nutrients in these lakes. A five-year study was conducted on the diatom community and environment in Lake Fuxian, China's largest deep freshwater lake, which is becoming eutrophic. The results indicate a shift in the diatom community from a stable state dominated by a single species to a rapid seasonal fluctuation, and there is a significant increase in diatom biomass. Specifically, stable stratification and low nutrient concentrations are limiting the growth of diatom biomass and maintaining the dominance of Cyclotella . Nutrients in the hypolimnion were replenished in the epilimnion during the extreme cold of winter, triggering a shift in the diatom community. This shift may imply that future climate change will exacerbate the positive feedback of hypoxia-nutrient release of algal blooms, potentially triggering a regime shift in the ecosystem of the entire lake. This study underscores the fact that climate change alters the internal feedback mechanisms of deep lakes, reducing ecosystem stability, and provides a scientific basis for further clarification of protection measures for deep lakes.