Objective To evaluate the effect of flexible endoscope channel automated brushing system on the disinfection quality of digestive endoscopes. Methods 160 pieces of endoscopes after gastroenteroscopy in the digestive endoscopy center of a hospital were chosen. According to the blocked randomization method, endoscopes were randomly assigned to the experimental group and the control group in a ratio of 1:1. During the endoscope channel brushing, endoscopes in the experimental group were brushed with flexible endoscope channel automated brushing system, while endoscopes in the control group were cleaned manually by cleaning and disinfection personnel. Diffe-rences in disinfection qualification rate of endoscopes, brushing time of endoscope channels, and physical fatigue of cleaning and disinfecting personnel between the two groups were compared. Results The overall qualification rate of endoscope disinfection in the experimental group was higher than that in the control group (98.75% vs 88.75%, P=0.009), with the qualification rate of gastroscope disinfection in the experimental group being higher than that in the control group (98.33% vs 86.89%, P=0.016). There was no statistically significant difference in the qualification rate of enteroscope disinfection between two groups (100% vs 90.00%, P=0.299). The brushing time of the endoscope channel in the experimental group was longer than that in the control group ([158.76±17.46] seconds vs[117.44±13.59] seconds, P < 0.001). The difference in physical fatigue scores of the cleaning and disinfection personnel before and after brushing in the experimental group was lower than that in the control group ([0.87 ±0.80] points vs[2.84 ±1.08] points, P < 0.001), there was no statistically significant difference in the physical fatigue scores of the cleaning and disinfection personnel before brushing between the two groups ([1.23±0.50] points vs (1.20±0.46] points, P=0.743);the physical fatigue scores of the cleaning and disinfection personnel after brushing in the experimental group were lower than that in the control group ([2.10 ±1.13] points vs[4.04 ±1.36] points, P < 0.001). Conclusion The flexible endoscope automated channel brushing system can improve the quality of endoscope disinfection and reduce the physical fatigue of cleaning and disinfection personnel.