Objective To monitor the microbial contamination of flexible endoscopes at different storage time after disinfection, so as to explore the safe storage period of flexible endoscopes. Methods 27 flexible endoscopes were selected from the endoscopy center of a tertiary first-class hospital in Chongqing by convenient sampling, a prospective study was performed, from October 2017 to February 2019, endoscopes with qualified biological monitoring after disinfection were stored at room temperature for 24, 48, 72 and 168 hours, bacterial colonies and qualified rate of bacterial colonies in the lumen and surface of endoscopes as well as air and surface of endoscope cabinets were monitored. Results Qualified rates of bacterial colonies in lumen and surface of 108 times of endoscopes stored for 24, 48, 72 and 168 hours were all 100%, the number of surface colonies in 108 times of endoscopes stored for 24, 48, 72 and 168 hours were all 0; the number of lumen colonies in 108 times of endoscopes stored for 24, 48, and 72 hours were all 0; the number of lumen colonies in 107 times of endoscopes stored for 168 hours were all 0; the number of lumen colony in 1 endoscopes stored for 168 hours was 6 CFU/piece, but without pathogenic bacteria. Qualified rates of colonies in air and object surface of endoscope cabinets were both 100%. Conclusion It is safe to store flexible endoscope in the qualified environment for 168 hours after high level disinfection, and it is unnecessary to disinfect it before use.