Surface area is one of the critical indicators of the intensity of cyanobacterial blooms in lakes and reservoirs, and its changes are affected by a combination of factors, such as the nutrient status of the water body, hydrometeorological conditions, and the structure of the food chain. Revealing the relationship between the area of cyanobacterial bloom and environmental factors is of great significance for the scientific assessment of the intensity of cyanobacterial bloom and the formulation of preventive and control measures. Based on the cyanobacterial bloom area data inverted from 2332 satellite remote sensing images of Lake Taihu from 2003 to 2023, combined with the nutrient salts of the lake and hydrometeorological observation data during the same period, this study explored the main environmental factors affecting the area of cyanobacterial bloom and their intra-annual changes in Lake Taihu. The results showed that the annual mean cyanobacterial bloom area of Lake Taihu was 159 km from 2003 to 2023, of which the multi-year mean value of the bloom season (May to September) was 223 km. The area of the cyanobacterial bloom was significantly correlated with the chlorophyll-a and microcystin biomass in the same period, with correlation coefficients of 0.47 and 0.48, respectively, indicating that the area of the cyanobacterial bloom obtained from remote sensing can better characterize the overall situation of the intensity of the cyanobacterial bloom. The annual average area of cyanobacterial blooms in Lake Taihu from 2003 to 2023 generally showed cyclic fluctuations, which could be roughly divided into four stages: (1) The area of cyanobacterial bloom firstly increased and then decreased from 2003 to 2008, with significant fluctuation; (2) The overall area of cyanobacterial bloom from 2009 to 2015 was low, with slight change; (3) The area of cyanobacterial bloom from 2016 to 2020 was increased, with high fluctuation; (4) The area of cyanobacterial bloom from 2021 to 2023 showed a rapid decreasing trend, in which the annual mean area of bloom in 2023 was 77 km , and the mean area of the bloom season was 116 km , which is the lowest value in the study period. The concentrations of total nitrogen (TN) and dissolved total nitrogen (DTN) in the water body of Lake Taihu from 2005 to 2023 declined significantly, with the average value of TN decreasing by 61% and DTN decreasing by 65% in 2023 compared with that of 2005, and total phosphorus (TP) and dissolved total phosphorus (DTP) also showed fluctuating downward trends. Random forest analysis showed that the environmental factors affecting the area of cyanobacterial blooms varied seasonally, with the dominant factor in spring being water temperature, followed by TP and wind speed; whereas in summer, the dominant factor was wind speed, followed by DTN and water level; in autumn, the dominant factor was wind speed, followed by TN and water level; and in winter, the dominant factor was wind speed, followed by DTN and DTP, and, specifically, on the monthly scale, the area of cyanobacterial blooms factors also showed inter-monthly differences. Based on the relationship between the area of cyanobacterial bloom and the TN and TP of the water body, if we want to control Lake Taihu to be in the condition of no noticeable bloom with high probability (monthly average cyanobacterial bloom area is less than about 5% of the lake area, set at less than 103 km for Lake Taihu), it is recommended that the control thresholds for TN and TP in winter and spring should be 1.35 mg/L and 0.054 mg/L, respectively, corresponding to 1.03 mg/L for DTN and 0.018 mg/L for DTP; the control thresholds for TN and TP in summer and autumn are 1.00 mg/L and 0.059 mg/L, respectively, corresponding to 0.62 mg/L for DTN and 0.015 mg/L for DTP. The study shows that the area of cyanobacterial bloom obtained from remote sensing image inversion can be a good indicator of the intensity of cyanobacterial bloom in large lakes; the area of cyanobacterial bloom in Lake Taihu is greatly affected by the change of wind speed in summer and autumn seasons, but the level of nitrogen, phosphorus and other nutrient is also an essential factor influencing the change of the area of cyanobacterial bloom, among which the effect of phosphorus is significant in winter and spring, and the effect of nitrogen is significant in summer and autumn; the implementation of nitrogen-phosphorus dual-control is the fundamental way of effectively reducing the risk of cyanobacterial bloom in the control strategy. Implementation dual control of nitrogen and phosphorus is a fundamental way to reduce the risk of cyanobacterial bloom.