Objective To understand the influencing factors for disinfection efficacy of gastroscope in county-level medical institutions of a province. Methods Nine secondary county-level comprehensive medical institutions were selected, questionnaire survey and on-site inquiry were adopted to fill in the questionnaire, on-site observation on cleaning and disinfection was conducted, intervention measures were taken against possible risk factors. Cleaning and disinfection efficacy of gastroscope before and after intervention was compared. Results 45 specimens of gastroscope were taken before and after intervention, qualified rates of gastroscope cleaning and disinfection before and after intervention were 11.11% and 100% respectively, difference was statistically significant (χ²=72.00,P<0.001). Multivariate logistic regression analysis showed that whether installed rational cleaning and disinfection equipment (OR=23.813), whether the cleaning and disinfection process met the specifications (OR=13.223), whether knowledge and skills of gastrocope were mastered proficiently (OR=9.265), whether cleaning and disinfection tools were equipped rationally (OR=7.745), whether detergent and disinfectant were used correctly (OR=0.076) were independent influencing factors for gastroscope disinfection efficacy. Conclusion The qualified rate of gastroscope cleaning and disinfection in county-level medical institutions is low, it is necessary to rationally equip cleaning and disinfection equipment and tools, strengthen training, standardize the cleaning and disinfection process as well as the use of detergent and disinfectant, and improve the relevant knowledge level of staff.