To reveal Microcystis aeruginosa colony formation mechanism and provide the basis for effectively controlling the algae blooming in the Three Gorges Reservoir region, impacts of N, P concentrations, Ca²⁺ concentration, light intensity and temperature on the growth, extracellular polysaccharides synthesis and colony formation of the M. aeruginosa were investigated, and the morphological characteristics of single cells and M. aeruginosa groups were compared. The results showed that the biomass of M. aeruginosa and EPS concentration increased with the increasing of N, P concentrations. The optimal Ca²⁺ concentration for the growth of M. aeruginosa was 65 mg/L, and the EPS content decreased with the increasing of Ca²⁺ concentration. High Ca²⁺ concentrations might stimulate the cells to secrete the EPS and simultaneously promote the EPS to be dissolved. Both Ca²⁺ and EPS took the responsibility for the colony formation of M. aeruginosa as the bridge bond action. Light and temperature played a role on the synthesis of the EPS, which were stronger than the promoting effects of N, P and Ca²⁺ concentrations. 20℃ was the most favorable temperature conditions for the Microcystis growth and EPS synthesis. The surrounding gelatinous sheath of cells group was more obvious and clearer than the single cell. Many Ca²⁺ crystals on the sheath surface of polysaccharide gums were observed. Thus, Ca²⁺ played an important role in EPS synthesis and colony formation.