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In this paper, a novel plasma reactor with high-voltage pulsed discharge in water through pinhole was proposed to treat algae. It produced multiple effects, i.e., shock waves, ultraviolet light, hydroxyl radicals, and strong electric field at the same time. In this paper, the killing effect of different alga was studied. The results showed that the inactivation rate reached 100%, where Chlorophyta was the most difficult to treat, the diatom the second, and Chrysophyte was the easiest. Platymonas spp. was more difficult to treat than Chlorella among the Chlorophyta. The chlorophyll a in the treated algae solution decreased with the increase of peak voltage. The result also showed that there were no differences between the two measurement methods for the survivability of algae: the optical microscope and spectrophotometer.