Abstract: The effects of chelerythrine on the growth, pigments contents and photosynthetic system of Microcystis aeruginosa NIES-843 were studied in this paper. The results indicated that the growth of M. aeruginosa NIES-843 was inhibited by chelerythrine at the concentration of 10 g/L. Regression analysis showed that the EC50 of chelerythrine on the growth of M. aeruginosa NIES-843 was (30.621.32) g/L. Intracellular pigments of M. aeruginosa NIES-843 decreased at the concentration of 160 g/L. Results of chlorophyll fluorescence transient analysis suggested that the absorbed energy (ABS/RC), the trapped energy for reduce of QA (TR0/RC) and the trapped energy for electron transport (ET0/RC) were all inhibited by chelerythrine. Energy fluxes ratios analysis of PSⅡ indicated that the electrons providing side of reaction centre was the targets of toxicity of chelerythrine on M. aeruginosa NIES-843.