Abstract: Microcystis aeruginosa often threatens human health and safety for its microcystin and bad smell. Its large number and hardness of removal are difficulty for water treatment. In this study, electron beam generated by an accelerator was applied to irradiate Microcystis aeruginosa by dose of 1, 2, 3, 4 and 5 kGy. The effect of irradiation on Microcystis aeruginosa characteristic and mechanism was studied by surveying the changing of protein, enzyme activity and photosynthesis rate. The data show that irradiation of 1 kGy has little effect on dissoluble protein, POD and SOD activity. Irradiation of 2-5 kGy can decrease protein content and destroy the antioxidant system, also the photosynthesis rate decreases obviously, which makes Microcystis aeruginosa lose activity in short time. The result proves that a certain dose of electron beam irradiation can control algae growth and affect its life characteristic efficiently.