Microcystis aeruginosa (Kütz.) Kütz. commonly occurs as single cells at early recruitment but forms large colonies in summer. Colony formation will induce many acclimative changes. In this study, we demonstrated the photochemical changes before and after colony formation. In the laboratory, light curves showed that colonies were more responsive to high light than single cells. The values of the maximal slope of electron transport rate (ETR)—light curve (α), relative maximal electron transport rate (rETRmax), and onset of light saturation (Ik) of colonies were significantly higher than those of single cells (P < 0.05), indicating that colonies have higher photosynthetic capability than single cells, especially in high light, where values of rETRmax and Ik of colonies were 2.32 and 2.41 times those of single cells. Moreover, the dark-light experiments showed that colonial cells can more effectively resist darkness damage. In addition, pigments of colonial cells were higher than those of single cells (P < 0.05). The higher pigment contents probably contribute to higher photosynthetic capability. In the field, the inhibition rate of Fv/Fm in single cells increased significantly faster than that of colonies as light increased (P < 0.05), but nonphotochemical quenching (NPQ) value of colonies was higher (32.4%) than that of single cells at noon, which indicated colonial cells can more effectively resist high-light inhibition than single cells (P < 0.05). Polysaccharides of colonies were significantly higher compared to those in unicellular cells (P < 0.05) based on their contents and ultrastructural characteristics. This finding implies that colonies could not effectively decrease photoinhibition by negative buoyancy regulation. In fact, NPQ may be an important mechanism for avoiding photodamage. All of these phenomena can help explain the ecological success of colonial M. aeruginosa in eutrophic water.