Physical filtration technique has been widely used throughout the world as a control for cyanobacteria. However, few studies have addressed the time and strength of the filtration making it a challenge to provide effective support for the filtration of cyanobacteria. Therefore, it is urgent to study the control feedback effect of cyanobacteria after physical filtration with different control intensities. In this study, through laboratory simulation experiments, the growth feedback rule of Microcystis aeruginosa, a dominant species of cyanobacteria in Lake Tai Basin, was systematically studied following different intensity physical filtration at various growth stages. Based on the results, the optimal control period and control intensity of cyanobacteria were proposed. The results showed that the growth of Microcystis aeruginosa conforms to the Logistic growth model. Physical filtration in the early and late stages of the Logistic start period was effective in inhibiting Microcystis aeruginosa, while filtration and inhibition in the early and middle stages of Logistic accelerated period were not effective. The growth of Microcystis aeruginosa was affected by different control intensity at different stages and can be effectively inhibited by 20-40% controlled intensity filtration in the early and late stages of the Logistic start period. If cost and environmental benefits are considered, we recommend the implementation of physical filtration at a minimum of 20% control intensity at the beginning of the Logistic start period.