Deep lakes are critical for freshwater storage, although they are struggling against major ecological issues from climate change and nutrient pollution. A comprehensive understanding of internal feedback mechanisms would be helpful for nutrient regulation within such lakes. A five-year consecutive study of the diatom community and its abiotic environment was conducted in Lake Fuxian, which is the largest deep freshwater lake in China and is currently heading toward a eutrophic state. The results indicate a shift in the diatom community from a stable state dominated by a single species to a rapid seasonal fluctuation, along with 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 and reduces the stability of their ecosystems, and provides a scientific basis for further clarification of protection measures for deep lakes.