Heatwaves are increasing and expected to intensify in coming decades with global warming. However, direct evidence and knowledge of the mechanisms of the effects of heatwaves on harmful cyanobacteria blooms are limited and unclear. In 2022, we measured chlorophyll-a (Chla) at 20-s intervals based on a novel ground-based proximal sensing system (GBPSs) in the shallow eutrophic Lake Taihu and combined in situ Chla measurements with meteorological data to explore the impacts of heatwaves on cyanobacterial blooms and the potential relevant mechanisms. We found that three unprecedented summer heatwaves (July 4-15, July 22-August 16, and August 18-23) lasting a total of 44 days were observed with average maximum air temperatures (MATs) of 38.1 ± 1.9 °C, 38.7 ± 1.9 °C, and 40.2 ± 2.1 °C, respectively, and that these heatwaves were characterized by high air temperature, strong PAR, low wind speed and rainfall. The daily Chla significantly increased with increasing MAT and photosynthetically active radiation (PAR) and decreasing wind speed, revealing a clear promotion effect on harmful cyanobacteria blooms from the heatwaves. Moreover, the combined effects of high temperature, strong PAR and low wind, enhanced the stability of the water column, the light availability and the phosphorus release from the sediment which ultimately boosted cyanobacteria blooms. The projected increase in heatwave occurrence under future climate change underscores the urgency of reducing nutrient input to eutrophic lakes to combat cyanobacteria growth and of improving early warning systems to ensure secure water management.