The ultraviolet (UV)/titanium dioxide (TiO2)/hydrogen peroxide (H2O2) process (UTHP) has been proven to be effective in removing organics because of its high production of free radicals. In this study, UTHP was further investigated for the photocatalytic degradation of microcystin-LR (MC-LR). Results showed that three mechanisms could realize MC-LR photocatalytic degradation using TiO2. H2O2 could effectively inhibit recombination and considerably improve the production of radicals and superoxides. From a correlation of the removal rate with the isomerization and decomposition of MC-LR under UV irradiation it was inferred that isomerization was crucial for MC-LR degradation during photocatalysis given the vulnerability of the exposed conjugated double bonds. The photocatalysis of MC-LR was apparently dependent on pH and MC-LR initial concentration. Under the optimum conditions of pH 3.5, 0.05 g/L TiO2, and 0.05 mmol/L H2O2, 100% MC-LR (308 μg/L) could be removed within 60 min. This process was accompanied by a synergistic effect during the initial 10 min.