Active chlorine（chlorine and hypochlorite） was generated with NaCl electrolytes by mixed metal oxide（IrO2-Ta2O5/Ti） electrode to inactivate Microcystis aeruginosa. The generation of active chlorine abides by the Faraday's law, and its concentration is proportional to the applied current density and reaction time. The variation of integrity, surface morphology, and photosynthetic ability of Microcystis aeruginosa during the electrochemical oxidation processes（EOPs） were investigated, and the release and degradation of algal organic matters and microcystins （MC-LR） were also studied. The results indicat that the EOPs can effectively inactivate Microcystis aeruginosa, and the proportion of cell lysis increases with current density and reaction time. The concentration of extracellular MC-LR during the EOPs increased and then decreased to below 1.0 μg·L-1. The EOPs can not only inactivate Microcystis aeruginosa，but also control the concentrations of algal organic matters and MC-LR. Therefore，the EOPs have a promising application potential for treating algae-laden water.