Cyanobacteria blooms in source waters have become a worldwide issue for drinking water production. UV-activated persulfate (UV/PS) technology was firstly applied to remove cultivated Microcystis aeruginosa (M. aeruginosa) in bench scale. The presence of persulfate significantly enhanced both cytoclasis and algal organic matter mineralization compared with UV-C inactivation alone. Around 98.2% of algal cells were removed after UV/PS process treatment for 2h at a dosage of PS being 1500mg/L (approximately 6mM). Both sulfate and hydroxyl radicals were proven to contribute to the removal of algae and the loss of cell integrity. The cultivated M. aeruginosa in death growth phase were found to be more vulnerable to UV/PS treatment than those growing in log phase, thus a significant lower dosage of PS is needed to achieve the desired removal efficiency. This study suggested a novel application of UV/PS process in the removal of algae in source waters due to the high degradation efficiency of both algal cells and their derived organic matter.