A microcystin detection and Environmental Scanning Electron Microscope investigation were carried out to analyze the microcystin removal effect and the forms of Microcystis aeruginosa cells with different dosage of potassium permanganate loaded zeolite. The results showed that potassium permanganate loaded zeolite had significant microcystin-LR removal effect both in the Microcystis aeruginosa and Nostoc samples. The optimal dosage and the optimal removal rate were 96.0% at 220mg/L and 77% at 110mg/L separately. The cell wall of Microcystis aeruginosa was ruptured by dosing both potassium permanganate and potassium permanganate loaded zeolite, while algae cells were accumulated. Cell groups treated by potassium permanganate loaded zeolite appeared more compact to improve cells settling performance and wrapped exudates to avoid microcystin excessing into water. There were abundant adsorption sites to adsorb intracellular and extracellular microcystin after potassium permanganate released from zeolite.