The experiments were performed to investigate the degradation of microcystins in order to assess the effectiveness and feasibility of UV/H2O2 system for the disinfection of water polluted by microcystins. The influence factors such as H2O2, pH and UV light intensities were investigated respectively. Degradation of microcystin-RR (MC-RR) could be fitted by either the pseudo-first-order or second-order rate equations. This homogenous system could significantly enhance the degradation rate due to the synergetic effect between UV and H2O2. The degradation mainly followed the mechanism of direct photolysis and .OH oxidation reactions. Experimental results showed that 94.83% of MC-RR was removed under optimal experimental conditions and the UV/H2O2 system provided an alternative to promote the removal of microcystins in drinking water supplies.