Growth of colonial Microcystis aeruginosa was investigated by performing an incubation experiment. Colonies of M. aeruginosa were separated based on size (colony diameter <100 μm, 100–200 μm and >200 μm) by filtration. Additionally, the cells around the surface of the colonies were separated from those inside the colonies by short-term ultrasonic treatment followed by filtration. Experimental results indicate that M. aeruginosa grew continuously throughout a 35-day incubation period in a nutrient-rich medium at specific growth rates between 0.045 and 0.310 d−1. On day 14, larger colonies exhibited insignificantly higher specific growth rates. However, on day 35, the specific growth rates of colonies with diameters less than 100 μm insignificantly exceeded those of larger colonies. Internal cells of the colonies tended to grow faster than peripheral cells. Furthermore, the specific growth rates of the cells that comprised colonies with diameters of below 200 μm exceeded those of peripheral cells. These results suggest a potential growth strategy of M. aeruginosa in maintaining a high growth rate, eventually leading to the dominance of large colonies, which have notable ecological advantages over smaller ones.