Objective To explore the disinfection effect of ozone combined with peracetic acid (PAA) on reducing the total number of aerobic bacteria in pure water from the terminal of centralized pure water supply system. Methods A two-stage controlled study was conducted, and microbial limit test was performed on the pure water from the terminal of centralized pure water supply system in a hospital. At the first stage, PAA disinfection method was adop-ted, and ozone enhanced disinfection (PAA combined with ozone disinfection) was adopted at the second stage. Disinfection effects at different stages were compared. Results A total of 211 water specimens were collected for testing, including 101 specimens from PAA disinfection group and 110 from ozone enhanced disinfection group. The bacterial colony qualification rate of terminal pure water from the ozone enhanced disinfection group was higher than PAA group ( 85.45% vs 74.26%, P=0.04). The median of aerobic bacterial colony number of the ozone enhanced disinfection group (2 CFU/mL) was significantly lower than that of the PAA disinfection group (20 CFU/mL). With time increase after disinfection, the number of aerobic bacteria colony in water specimens from the PAA disinfection group showed a significant upward trend (Day 1 vs Day 92: 9 CFU/mL vs 1 062 CFU/mL), while the aerobic bacteria fluctuation range in the pure water from the ozone enhanced disinfection group was relatively small (Day 1 vs Day 92: 8 CFU/mL vs 58 CFU/mL). Conclusion The ozone combined with PAA disinfection method can significantly reduce the total number of aerobic bacteria in water from the terminal of centralized pure water supply system, with obvious maintaining effect.