Objective To explore the intervention efficacy of antimicrobial stewardship (AMS) on antimicrobial prophylaxis during peri-operative period of digestive endoscopy of patients. Methods A total of 1 006 patients who underwent digestive endoscopy in a hospital from January to June 2019 were included in the study, AMS strategy was adopted to manage antimicrobial prophylaxis during peri-operative period, these measures included establishing organization, improving policies, optimizing hospital information system, conducting education and training, as well as performing continuous intervention and supervision. 822 patients who underwent digestive endoscopy from January to June 2017 were as control group, changes in peri-operative prophylactic antimicrobial use rate, antimicrobial use density (AUD), as well as varieties, combination use and duration of antimicrobial use between two groups of patients were compared and analyzed; irrational use of antimicrobial agents and post-operative infection between two groups were also compared. Results Prophylactic antimicrobial use rate before and after intervention were 24.82% (204/822) and 17.10% (172/1 006) respectively, difference before and after intervention was statistically significant (P < 0.001); AUD was 2.18 after intervention, which was lower than 14.95 before intervention; proportion and duration of combined medication were also significantly lower than those before intervention. After the implementation of AMS strategy, irrational use rate of antimicrobial agents was lower than that before the implementation (P < 0.001); there was no significant change in the incidence of infection after operation (P>0.05). Conclusion AMS strategy can optimize antimicrobial prophylaxis during peri-operative period of digestive endoscopy.