Microcystis development in most temperate lakes shows an annual cycle that is mainly triggered by water temperature and includes four stages. This study aims to identify the optimum growth temperature and the temperature thresholds for recruitment and overwintering in Microcystis in Lake Taihu, based on field data and experiments at the cellular and genetic level on Microcystis under a simulated temperature condition. The field investigation showed that the cyanobacterial biomass began to increase at 11-15 °C in spring, reached a peak at 20-30 °C and remained at a low level after the water temperature declined below 6 °C. The simulation experiment found that the recovery of gene expression, photosynthesis and growth in Microcystis cells occurred at 11-14 °C and increased to an appreciable level after the temperature exceeded 20 °C. Microcystis cells stopped growing and maintained low photosynthetic activity and gene expression when the temperature declined to 10 °C or lower. These results suggest that Microcystis in Lake Taihu begin recruitment at 11-14 °C in spring and grow vigorously at 20-30 °C, then overwinter at 10 °C or lower in winter.