Electron beam irradiation was applied to control and eliminate the growth of Microcystis aeruginosa, and the effects of different irradiation doses on the physiological activity of algae cell was studied through scanning the changes of the respiratory rate and antioxidant enzyme activity of the algae. The results show that the electron beam radiation makes Microcystis aeruginosa suffer severe persecution, and its respiratory rate and antioxidant enzyme activity increase firstly and then decrease under the condition of adverse circumstances. It also show that the irradiation doses of 3~5 kGy damage the algae most severely, its antioxidant enzyme activity decreases after irradiation intimidating, the equilibrium between the production and elimination of active oxygen in the algae cell is broken; then the oxidized damage comes, and the extracellular exopolysaccharide reduces. It was found that the radiation of low dose could reduce the algal physiological activity and control its growth, and the radiation doses of 3~5 kGy could make algae cell lose its activity in a short time and eliminate them efficiently.