Harmful cyanobacterial bloom is one of the serious environmental problems worldwide. Microcystis aeruginosa is a representative harmful alga in cyanobacteria bloom. It is of great significance to develop new technologies for the removal of Microcystis aeruginosa and microcystins. The feasibility and mechanism of removing microcystis aeruginosa and degrading microcystins by dielectric barrier discharge (DBD) plasma were studied. The suitable DBD parameters obtained in this study are DBD (41.5 W, 40 min) and DBD (41.5 W, 50 min), resulting in algae removal efficiency of 77.4% and 80.4%, respectively; scanning electron microscope and LIVE-DEATH analysis demonstrate that DBD treatment can disrupt cell structure and lead to cell death; analysis of elemental composition and chemical state indicated that there are traces of oxidation of organic nitrogen and organic carbon in microcystis aeruginosa; further intracellular ROS concentration and antioxidant enzyme activity analysis confirm that DBD damage microcystis aeruginosa through oxidation. Meanwhile, DBD can effectively degrade the microcystin-LR released after cell lysis, the extracellular microcystin-LR concentration in the DBD (41.5 W) group decreased by 88.7% at 60 min compared to the highest concentration at 20 min; further toxicity analysis of degradation intermediates indicated that DBD can reduce the toxicity of microcystin-LR. The contribution of active substances to the inactivation of microcystis aeruginosa is eaq− >•OH > H2O2 > O3 > 1O2 >•O2− >ONOO−, while on the degradation of microcystin-LR is eaq− >•OH > H2O2 > O3 >•O2− >1O2 > ONOO−. The application of DBD plasma technology in microcystis aeruginosa algae removal and detoxification has certain prospects for promotion and application.