Chironomus kiiensis larvae which cannot be exterminated by conventional disinfection process propagates prolifically in eutrophic water body, and it therefore turns to be a potential problem encountered in drinking water quality. In order to tackle this problem, a pilot-scale study of removal effect on Chironomus kiiensis larvae with chlorine dioxide in a waterworks is performed. The experiment results showed that Chironomus kiiensis larvae can be effectively removed from water by 0.55 mg/L chlorine dioxide pre-oxidation combined with the conventional drinking water treatment process. Higher oxidizability and molecular state of chlorine dioxide in water is the key to the inactivation of Chironomus kiiensis larvae. The chlorite, disinfection by-products (DBPs) of chlorine dioxide, is stable at 0.217 mg/L, which is lower than that critical value of the WHO. Ames test revealed that the mutagenicity was reduced by chlorine dioxide with respect to prechlorine. The propagation of Chironomus kiiensis larvae can be inactivated effectively and safely by chlorine dioxide pre-oxidation.