The inactivation effect of chloramine, chlorite for ammonia-oxidizing bacteria and heterotrophic bacteria was compared by using rotating annular bioreactors (RAB), which were applied to simulate the drinking water distribution system. The experiment results showed that 1.5 mg/L chloramine had a higher inactivate rate to AOB in bulk water (5.7×10-2 log/h) than in the biofilm (4.8×10-2log/h) during 24 h. Compared with chloramine, 0.6 mg/L chlorite had a much higher inactivation rate to AOB in the biofilm (6.4×10-2log/h) and bulk water (7.2×10-2log/h). Chlorite and hybrid of chlorite and chloramine disinfection had almost the same inactivation efficiency, and chlorite had no inactivation effect on heterotrophic in the biofilm and bulk water. The inactivation rate of chloramine on heterotrophic bacteria was 8.3×10-2log/h and 5.5×10-2log/h respectively. Based on chlorite inactivation effect on AOB and chloramine on heterotrophic bacteria, the hybrid disinfection of chloramine and chlorite on the controlling of nitrification was put forward.