Objective To describe the current state of hospital infection prevention and control for flexible endoscope in Shanghai, and analyze the trend of infection prevention and control quality from 2018 to 2022. Methods According to Regulation for Cleaning and Disinfection Technique of Flexible Endoscope (WS 507－2016), the quality of infection prevention and control for flexible endoscope was divided into seven parts: organizational management, layout, cleaning and disinfection (sterilization) process, environmental disinfection and sterilization, final rinse water, recording and monitoring, and occupational protection. Each quality control item was judged according to the on-site score and the correction opinion, and the item with correction opinion was judged as “unqualified”, otherwise it was “qualified”. The results of the infection prevention and control quality supervision for flexible endoscope from 2018 to 2022 were reviewed and analyzed, and the qualification rates of quality control items for hospitals at different levels and in different years were calculated. Results From 2018 to 2022, the total qualification rates of organization management, final rinse water, environmental disinfection and sterilization, and occupational protection were over 90%, and the total qualification rates of cleaning and disinfection (sterilization) process, and records and monitoring were over 80%. There was no statistically significant difference in the annual qualification rate (P>0.05). The total qualification rate of the layout was 78.19%, which was significantly higher before the outbreak of COVID-19 (2018-2019) than after the outbreak of COVID-19 (2020-2022) (P<0.001). There was no significant difference in the qualification rate of different levels of hospitals in terms of organizational management, layout, cleaning and disinfection (sterilization) process, records and monitoring, or occupational protection item (P>0.05). There were statistical differences in the qualification rates of different levels of hospitals in terms of final rinse water and environmental disinfection and sterilization (P<0.05). Conclusions The infection prevention and control qualification rate of flexible endoscope in Shanghai is high. However, the layout qualification rate after the COVID-19 pandemic is lower than before. There has been no significant trend in the quality of other items in the past five years. Weaknesses in the cleaning and disinfection (sterilization) process, as well as in recording and monitoring, are identified as key areas in management. Targeted training and supervision are recommended to address these weaknesses.