Abstract: Metsulfuron-methyl is one of the sulfonylurea herbicides, which have been widely used throughout the world because of its significant advantages and safety. However, long-term use of Metsulfuron-methyl will impose a threat to aquatic ecosystems. Algae are frequently the major primary producers in aquatic ecosystems, often as an indicator to study water pollutants. In this study, dominant species of cyanobacteria (Microcystis aeruginosa PCC7806) were selected to deeply perceive the effect of Metsulfuron-methyl on the growth and photosynthetic of Microcystis aeruginosa. The achieved results showed that the growth of M. aeruginosa PCC7806 was significantly inhibited when the concentration of Metsulfuron-methyl exceeds 80 mg/L. The EC₅₀ of the growth of M. aeruginosa PCC7806 was 81.998 mg/L by regression and Probit analysis. The results of cytochrome studies demonstrated that the content of chlorophyll a and carotenoids in unit cell of the treatment group on the 6th day was lower than that of in the control group, and when the concentration of Metsulfuron-methyl was 80 mg/L, the carotenoids content was remarkably lower than that of in the control group. The results of kinetics of chlorophyll fluorescence showed that the energy (ET₀/RC) captured by the unit reaction center for electron transport (φE₀) was used for quantum yield of photosynthetic of electron transport, which is extraordinary suppressed on the 6th day of the experiment. The results of chlorophyll fluorescence induction and cytochrome analysis showed that Metsulfuron-methyl could negatively affect the electronic properties of the electron acceptor in the photosynthetic reaction center. In summary, Metsulfuron-methyl may act on the electron acceptor side of the photosynthetic response center, thereby likely affecting the photosynthetic system of Microcystis aeruginosa.