This study aims to investigate the unexplored mesoscale mechanism that affects the horizontal migration and aggregation of Microcystis in Lake Taihu during algal bloom formation. Based on field measurements of water dynamics and Microcystis biomass, an IBM model(individual-based model) that considered the combined effects of wind and light on Microcystis migration was developed. The model was calibrated using various field data, and was used to simulate the process of algal bloom expansion that occurred multiple times in 2017. The results indicated that the vertical distribution of Microcystis under wind disturbance determined its horizontal migration speed, with closer proximity to the water surface resulting in faster migration speeds. In Lake Taihu, which was dominated by wind-driven currents, Microcystis exhibited three distinct horizontal migration patterns: slow migration of the upper layer under low winds, rapid migration of the upper layer under favorable winds, and consistent slow migration of the middle and lower layers. These patterns lead to long-term “horizontal migration accumulation” where Microcystis drifted faster towards the downwind bays and migrated slower out of them. This difference in migration rates resulted in a concentration effect of Microcystis in the downwind bay. This study provides important theoretical insights for a deeper understanding of the formation mechanism and prediction of Microcystis blooms in Lake Taihu, a crucial topic in environmental science and ecology.