In the context of global climate change, the frequency and intensity of extreme heat events (heat waves) have increased significantly, posing potential threats to the stability of lake ecosystems. To assess these impacts, this study simulated short-term heat waves using the Middle Universe Simulation System. A combined metagenomic and metatranscriptomic sequencing approach was applied to systematically examine structural and functional responses of lake aquatic microbial communities. The results showed that microbial community composition remained largely stable under short-term high-temperature stress, whereas functional diversity increased markedly, with 467 unique functions detected compared to the control group. Moreover, gene expression levels exhibited substantial changes, particularly in metabolic pathways and photosynthetic processes. The Bray–Curtis analysis further revealed an increase of 0.12 in community compositional distance and 0.16 in functional distance following heat wave exposure. These findings indicate that heat waves primarily affect aquatic ecological processes by driving shifts in functional diversity. Overall, aquatic microbial communities appear capable of rapidly adapting to environmental fluctuations through functional adjustments, while structural changes occur more slowly.