Colony formation is a crucial characteristic of Microcystis, a cyanobacterium known for causing cyanobacterial harmful algal blooms (cyanoHABs). It has been observed that as Microcystis colonies grow larger, they often become less densely packed, which correlates with a decrease in light penetration. The objective of this study was to investigate the effects of light limitation on the morphological variations in Microcystis, particularly in relation to the crowded cellular environment. The results indicated that when there was sufficient light (transmittance = 100 %) to support a growth rate of 0.11±0.01 day−1, a significant increase in colony size was found, from 466±15 μm to 1030±111 μm. However, under light limitation (transmittance = 50 % – 1 %) where the growth rate was lower than 0, there was no significant improvement in colony size. Microcystis in the light limitation groups exhibited a loose cell arrangement and even the presence of holes or pores within the colony, confirming the negative correlation between colony size and cell arrangement. This pattern is driven by regional differences in growth within the colony, as internal cells have a significantly lower frequency of division compared to peripheral cells, due to intra-colony self-shading (ICSS). The research demonstrates that Microcystis can adjust its cell arrangement to avoid excessive self-shading, which has implications for predicting and controlling cyanoHABs. These findings also contribute to the understanding of cyanobacterial variations and can potentially inform future research on the diverse phycosphere.