Large Microcystis colonies can lead to the rapid formation of surface accumulations, which are a globally significant environmental issue. Laboratory studies have shown that Ca2+ can quickly promote non-classical Microcystis colony formation via cell-adhesion, but our knowledge of the changes in the morphology of these colonies during subsequent long-term culture with Ca2+ is limited. In this study, a 72-day cultivation experiment was conducted to determine the long-term effects of Ca2+ on Microcystis colony formation. Laboratory results indicate that Ca2+ causes Microcystis to rapidly aggregate and form a colony through cell adhesion, then colony formation by cell-adhesion lost dominance, owing to the decrease in Ca2+ concentrations caused by precipitation/complexation. Although the initial colony morphology by cell adhesion is sparse, the newly divided cells, without separating from the mother cells, constantly fill the gaps in the original colony at Ca2+ concentrations >40 mg L−1 for a long time, which creates colonies on day 72 with a morphology similar to that of M. ichthyoblabe in Lake Taihu. If the Ca2+ levels in Lake Taihu continue to increase, Microcystis growth rate will decrease only slightly, while the colony proportion of total biovolume and biomass will increase. Moreover, higher Ca2+ concentrations do not affect microcystin content, but promote the content of bound extracellular polysaccharides (bEPS), enabling formation of larger colonies, which may promote Microcystis surface accumulation.