Objective To compare and analyze the efficacy and cost of endoscope cleaning and disinfection detected with membrane filtration method and smear method. Methods Endoscopes after cleaning and disinfection in a large tertiary first-class general hospital from January to December 2018 were randomly selected, cleaning and disinfection efficacy of endoscopes were detected with membrane filtration method and smear method respectively, the qualified rate, pathogen detection rate, bacterial colony count and cost between two methods were compared, QuestionStar^TM and WeChat platform were used to investigate the current status of detection methods for endoscope cleaning and disinfection efficacy in some hospitals. Results A total of 207 flexible endoscopes were detected. The qualified rates of endoscopes detected with membrane filtration method and smear method were 78.26% and 95.65% respectively, difference was statistically significant (P<0.001). After endoscopes were cleaned and disinfected, pathogen detection rate and bacterial colony count detected with membrane filtration method were both higher than smear method, difference was statistically significant (P<0.001). Compared with smear method, economic cost of 207 endoscopes detected with membrane filtration method increased by 1 498.48 yuan per year, with an average increase of 7.24 yuan per endoscope. On average, each endoscope detected with membrane filtration method took 62 seconds longer than smear method. A total of 26 hospitals were investigated endoscope cleaning and disinfection detection methods, only 2 hospitals adopted membrane filtration method. For membrane filtration method to detect the cleaning and disinfection efficacy of endoscopes, the most important issue concerned by hospitals was increased economic cost. Conclusion Membrane filtration method can effectively cultivate bacteria in the eluent of endoscopes and objectively reflect the cleaning and disinfection efficacy of endoscopes.