Algae in drinking water supplies often bring about impact on the water treatment. In this study, a bipolar pulsed dielectric barrier discharge system in three-phase discharge plasma reactor was constructed for investigating its ability to control excessive growth of cyanobacteria, Microcystis aeruginosa. Experimental results show there was almost no change in optical density immediately after the interruption of electrical discharge, but the decreasing trend of optical density, cell density and chlorophyll-a content was obvious during the incubation period, indicating a significant residual effect of electrical discharge process on the algal growth inhibition. Scanning electron microscopy investigation of algae revealed surface damage, apparent leakage of intracellular contents and pores formed after electrical discharge process, which showed that algal cells had no potential to survive and grow. Compared with the control sample, it was observed that electrical discharge on the algal extracellular products has almost no residual effect and the growth rate of algae slightly decreased before three days storage. Hydrogen peroxide was produced by electrical discharge in the mu M level and showed a first-order decay. But at such level, the external addition of hydrogen peroxide alone is not likely to cause the residual effect. These results implicated that the growth inhibition of M. aeruginosa was mainly caused by electrical discharge process, and it made the algal cells lose ability to survive, demonstrating the considerable potential of such an alternative process for efficient water purification.