Colony formation is an essential stage of cyanobacterial blooms. High calcium concentration can promote Microcystis aeruginosa aggregation behavior, but the mechanism of colony formation caused by calcium has rarely been reported. In this study, high calcium-induced colony formation was identified as a shift from cell adhesion to cell division, rather than only cell adhesion as previously thought. Algae responded to this calcium-induced environmental pressure by aggregating and forming colonies. Algal cells initially secreted large quantities of extracellular polysaccharides (EPS) and rapidly aggregated by cell adhesion. The highest aggregation proportion was up to 68.93%. However, high calcium concentrations cannot completely inhibit algal cell growth, but only delay the algae into the rapid growth phase. With adaption to calcium and existing high EPS content, the daughter cells reduced EPS synthesis and the aggregation proportion decreased. The increasing growth rate was also responsible for the decreased xylose content in EPS. The mechanism of colony formation changed to cell division. The downregulation of genes related to EPS secretion also supported this hypothesis. Overall, these results can benefit for our understanding of cyanobacterial bloom formation.