ObjectiveA tertiary first-class hospital installed a new purified water system, in order to ensure that the final rinse water in the digestive endoscopy center met the regulatory requirements, microbial monitoring was conducted on the main purified water pipeline and endoscope final rinse water. The causes of limit-exceeding of microbes were analyzed, and solutions were proposed to provide reference for disposal of similar incidents. Methods Water specimens from the automated endoscope reprocessor (AER) and cleaning workstation were collected, and microbial contamination level was analyzed. By implementing measures such as installing filter membranes, insta-lling ultraviolet lamp (UV) lamps, and conducting pipeline cleaning at AER and the front end of final rinse tank in endoscope cleaning workstations, bactericidal effects of different combinations of filtration-disinfection on microbes in purified water were evaluated to verify the feasibility of synergistic intervention of filtration-disinfection combination and pipeline disinfection. Results 0.2 μm filter membrane+0.45 μm filter membrane+UV lamp, 0.2 μm filter membrane+0.2 μm filter membrane, 0.2 μm filter membrane+0.2 μm filter membrane+UV lamp, and 0.1 μm filter membrane could all ensure the total number of bacteria in purified water entering AER and final rin-sing tank ≤10 CFU/100 mL. After the qualified purified water reaching AER and endoscope cleaning workstation, the total bacterial count in the final rinse water exceeded the limit. After disinfection AER and the pipelines of endoscope cleaning workstation, the microbial qualified rate of the final rinse water increased from 0 to 100%. Conclusion The synergistic strategy of optimizing the filtration-disinfection combination and conducting thorough pipeline clea-ning can effectively reduce microbial content in purified water, ensuring the safety of water used for flexible endoscopy diagnosis and treatment.