Abstract: Wind speed and solar irradiance are the important affecting factors that determine the vertical active and passive migration of cyanobacteria in shallow lakes due to the existence of gas vacuoles. Cyanobacteria can migrate vertically to occupy favorable ecological niches through adjusting the buoyancy of gas vacuoles in response to external factors such as wind, light, and predation. Therefore, cyanobacteria microorganisms often accumulate on the water surface, forming visible floating blooms that affect the landscape and threaten ecosystem health. While the extensive studies have been carried out to elucidate cyanobacterial vertical migration mechanisms, the scientific knowledge to finely characterize vertical migration of cyanobacterial and quantify the affecting factors based on field in situ observations is still limited. During the cyanobacteria outbreak in Lake Taihu from July to September 2022, ground-based hyperspectral proximal sensing instrument was used to capture the vertical migration and the floating of cyanobacteria on water surface on daytime and night based on high-frequency continuous observations. This study combined synchronous high-frequency meteorological data and scientifically quantified the impact of typical meteorological factors on the vertical migration of cyanobacteria through field in situ observations. Our results showed that: (1) Wind speed and solar irradiance were significantly and negatively correlated with the probability of floating cyanobacteria. (2) Wind speed had a dominant influence on floating cyanobacterial communities, with a contribution rate of 66.60%, while the contribution rate of solar irradiance was 29.92%. (3) Cyanobacterial communities exhibited a periodic vertical migration pattern, sinking during the daytime and floating up at night. (4) When cyanobacterial particles accumulated to form algal clusters, their vertical migration was less affected by wind and strong light. Therefore, the compound effects of wind speed and solar irradiance had a significant impact on the vertical migration, aggregation and dissipation of cyanobacterial communities. Our findings deepen the scientific understanding of the formation mechanism of cyanobacterial bloom and provide theoretical reference for cyanobacterial bloom forecasting, early warning, and disaster prevention.