Objective To discuss the disinfection effect of persistent hypochlorous acid supply to final rinse water for endoscope. Methods Water specimens of final rinse water for endoscope were collected at baseline, and identified by microbial culture and metagenomic next-generation sequencing (mNGS). After introducing a slightly acidic hypochlorous acid water generator, water specimens were collected at a specific time after installation for culture and mNGS analysis. Results A total of 27 water specimens were collected before installation, and 10 (37.03%) were qualified. Aquatic bacteria such as Rhizobiumradiobacter, Stenotrophomonas maltophilia, Microbacterium flavum, Cupriavidus, Methylobacterium fujisawaense and Sphingomonas paucimobilis can be detected in unqualified water specimens, 54 water specimens were collected after installation, and all of them were qualified. mNGS shows that abundant sequences of Ralstonia Pichia, Cupriavidus metallidurans, Moraxella osloensis, Rhizobium japonicum, Aquatic methylbacterium, Mycobacterium Gordon and Sphingosine neobacterium could be detected in water specimens before installation, but only background bacteria in mNGS were found after disinfection. Conclusion Persistent hypochlorous acid supply can effectively remove bacteria and reduce biofilm formation in water pipeline, improving the quality of final rinse water for endoscope.