In order to strengthen the management of disinfection quality of endoscopes, Quality Control Center of Digestive Endoscopy and Nosocomial Infection Control Center of Yunnan Province investigated the diagnosis, treatment, cleaning and disinfection conditions and disinfection quality of digestive endoscopes in some medical institutions of Yunnan Province by web questionnaire from April to May in 2019, and 277 valid questionnaires were finally obtained. SPSS 19.0 statistical software was used to analyze the influencing factors of cleaning and disinfection process and the infection control implementation of digestive endoscopes in 227 secondary and tertiary hospitals. The results showed that the number of decontamination people who had received systematic training in Yunnan Province was significantly lower than that in other areas of China. The hospital level, the number of decontamination personnel, and decontamination methods affected the implementation of cleaning and decontamination process and infection control, while the allocation of decontamination supplies had no effects. It is important to establish an effective mechanism for the normalized implementation of cleaning and disinfection of digestive endoscopes.