Dielectric barrier discharge (DBD) low temperature plasma was used to inactivate Microcystis aeruginosa. The effects of DBD low temperature plasma discharge conditions on Microcystis aeruginosa inactivation were investigated,such as discharge parameters, field structure parameters and solution liquid phase system factors, etc. Several analytical methods [e.g., acetone extraction spectrophotometry, conductivity measurement, scanning electron microscopy (SEM) and high performance liquid chromatography (HPLC)] were used to test the inactivation effect of Microcystis aeruginosa. The experimental results show that the discharge conditions have a great influence on the inactivation rate. Under the optimum conditions (discharge voltage 160 V, discharge current 0.63 A, dielectric spacing 4 mm, initial OD value of solution 0.2, pH value is weakly alkaline), discharge time 5 min, the inactivation rate of Microcystis aeruginosa can reach more than 90%. After discharge treatment, the color of Microcystis aeruginosa solution changed from bright green→light green→light yellow→colorless. The Chl-a content of Microcystis aeruginosa decreased significantly. The photosynthetic ability was inhibited, and the growth of Microcystis aeruginosa was blocked. SEM results showed that the algal cells were full and complete before discharge treatment. After discharge treatment, the cell structure of Microcystis aeruginosa was seriously damaged. The cell membrane was broken, and the cell content was leaked, which only left a small amount of cell debris. After discharge treatment, the electrolyte exudation rate of Microcystis aeruginosa increased. The cell membrane structure was seriously damaged, resulting in the increase of permeability and the leakage of cell contents. In the process of Microcystis aeruginosa inactivation, the content of microcystins first increased and then decreased with the discharge time. Under the optimum discharge conditions, after 5 min discharge treatment, not only the microcystins released by the rupture of Microcystis aeruginosa were completely degraded, whose removal rate was 100%, but also the microcystins in the original water were degraded. The above experimental results indicate that DBD low temperature plasma technology is a better method to remove Microcystis aeruginosa. This method can not only inhibit the proliferation of Microcystis aeruginosa, which has remarkable inactivation effect, but also will not cause secondary pollution of water body. So this method has good application value.