Genus Microcystis is the most common dominant species of bloom-forming cyanobacteria. Growth and colony formation are critical processes for the occurrence of Microcystis blooms. To identify allelochemicals that can inhibit the growth and colony formation of Microcystis, Microcystis aeruginosa was cultivated and treated with various concentrations of gramine, catechol, berberine, and sanguinarine in laboratory. Results indicate that the growth, colony formation, and extracellular polysaccharides (EPS) content of Microcystis were significantly inhibited when treated with gramine, catechol, and berberine in appropriate concentrations at high iron level (6.8 mg/L). Microcystis growth was inhibited and colony formation and EPS content were promoted when treated with sanguinarine at high iron level. These findings suggest that cyanobacterial blooms can be controlled by regulating the input of gramine, catechol, and berberine. Furthermore, this study revealed that plant allelochemicals could affect the growth and morphology of algae in aquatic ecological restoration, which may be potentially important for improving water quality.