Mesocyclops Leukarti of zooplankton propagates excessively in eutrophic water body and it can not be effectively inactivated by the conventional process in drinking waterworks for its special surface structure. In this paper, a study of removal efficiency on Mesocyclops Leukarti with chlorine dioxide in a drinking waterworks was performed.Bench scale results showed that chlorine dioxide is more effective against Mesocyclops Leukarti. And Mesocyclops Leukarti could be effectively removed from water by 1.0 mg/L chlorine dioxide preoxidation cooperated with the conventional process during the full scale study. The chlorite, by-preduct of prechlorine dioxide, was constant at 0.45 mg/L after filtration, which was lower than the critical value of the USEPA. GC-MS examination and Ames test showed that the quantity of organics and the mutagenicity in the water treated by chlorine dioxide is obviously less than that of prechlorination.