Objective To explore clean and disinfection effect of improved whole-pipe irrigation device on endoscope with auxiliary water supply. Methods The Olympus colonoscopes with auxiliary water supply used by patients in a digestive endoscope cleaning and disinfection workstation in a hospital was selected and randomly divided into three groups according to random number table method: group A, B, and C were 30, 32, and 30 respectively. Group A used the pre-improvement conventional irrigation device, and didn't perform special treatment to the auxi-liary water pipe; group B used the pre-improvement conventional irrigation device, but used the external connecting pipe (MAJ-855), for each cleaning and disinfection step, 30mL syringe was used to manually inject gas and liquid into the auxiliary water pipe for at least three times; group C used the improved whole-pipe irrigation device. Three groups of endoscopes were cleaned, disinfected and dried according to the standard steps, disinfection qualification rate of each pipe of three groups of endoscopes, as well as manual operation time and degree of physical fatigue of cleaning and disinfection staff and were compared. Results The overall qualified rate of endoscope disinfection in group A, B, and C were 30.0%, 78.1%, 100.0% respectively. There was significant difference in the overall disinfection qualified rate of endoscopes among three groups (χ²=36.414, P < 0.001). There was no significant difference in the disinfection qualified rate of endoscopic air and water supply pipe and forceps pipe among three groups (all P>0.05). There was significant difference in the disinfection qualified rate of endoscopic auxiliary water supply pipe among three groups (χ²=33.473, P < 0.001). The manual operation time of cleaning and disinfection staff in group A, B, and C were (4.81+0.63), (6.72+0.42), and (4.88+0.66) minutes respectively, difference was statistically significant (F=105.149, P < 0.001). The scores of physical fatigue scale of cleaning and disinfection staff for endoscope cleaning and disinfection in group A, B, and C were (4.67+1.32), (5.83+0.91), and (4.33+1.03) respectively, difference was significant among three groups (F=15.348, P < 0.001). Conclusion The improved whole-pipe irrigation device can improve the disinfection qualification rate of auxiliary water supply pipe, save the manual operation time of cleaning and disinfection staff and reduce their physical fatigue.