Microcystins (MCs) produced by cyanobacteria are strong hepatotoxins and classified as possible carcinogens. MCs pose a considerable threat to human health through tainted drinking and surface waters. Herein filtrated water from a waterworks in Harbin, China, was spiked with microcystin-LR (MC-LR) extracted from a toxic scum of microcystis aeruginosa, and the spiked sample waters were treated using UV irradiation with consequent ozonation process (UV/O3), compared with ozonation at a dose range commonly applied in water treatment plants, UV irradiation at 254 nm and UV irradiation combined with ozonation (UV+O3), respectively. The remaining of toxins were analyzed using high-performance liquid chromatography and also determined using a protein phosphatase type 2A inhibition assay, which was utilized to evaluate the reduction in toxicity. Results indicated that in comparison to other three processes (O3, UV, and UV+O3), UV/O3 process could effectively decrease both the concentration and toxicity of MC-LR at 100 microg/L level after 5 min UV irradiation with consequent 5 min ozonation at 0.2 mg/L (below 1 microg/L), while 0.5 mg/L ozone dose was required for the level below 0.1 microg/L. The addition of an UV treatment step to the existing treatment train may induce significant transformation of micropollutants and breaks down the natural organic matters into moieties unfavorable for ozone decomposition, stabilizing the ozone residual. These findings suggested that sequential use of UV and ozone may be a suitable method for the removal of these potentially hazardous microcystins from drinking water.