Objective To analyze the current status and existing problems of microbiological monitoring on duodenoscopes and linear array ultrasound endoscopes in China. Methods A convenience sampling method was used to conduct a questionnaire survey, titled "Questionnaire on the Current Status of Microbiological Monitoring of Duodenoscopes and Linear Array Ultrasound Endoscopes", among digestive endoscopy centers in 313 medical institutions (MIs) nationwide. The survey covered the implementation of microbiological monitoring, monitoring frequency, sampling methods, and result determination. Results The 313 tertiary MIs cover 27 provincial-level administrative regions. 97.76% of MIs performed microbiological monitoring on duodenoscopes and linear array ultrasound endoscopes, with monitoring frequency mainly being once a month (49.32%, 44.10%, respectively) and once a quarter (44.22%, 46.58%, respectively). Either full inspections (52.72%, 45.34%) or proportionately sampled inspections on a rotational basis (34.69%, 43.48%) were performed. Most MIs conducted biopsy channel sampling for duodenoscopes and linear array ultrasound endoscopes (91.50%, 93.79%, respectively), with common flushing method (83.22%, 78.48%, respectively) being the most common. Pump-assisted sampling (8.39%, 11.39%, respectively) and brush-assisted sampling (5.59%, 5.70%, respectively) were less used. Most MIs performed sampling of forceps with special structure for duodenoscopes and linear array ultrasound endoscopes (82.99%, 85.71%, respectively), primarily using the flushing method (56.15%, 52.17%, respectively). 65.99% of the MIs sampled the distal caps of duodenoscopes, with swab sampling (54.12%) being the primary method. For the determination of microbiological monitoring results of duodenoscopes and linear array ultrasound endoscopes, 60.20% and 58.39% of MIs used the quantity of microorganisms in the biopsy channel as the judgement criteria, while other MIs used the highest microbial number among multiple channels (sites) (26.87% and 29.19%, respectively) or the sum of microbial number in multiple channels (sites) (12.93% and 12.42%, respectively). Conclusion The standardization and implementation of microbiological monitoring on duodenoscopes and linear array ultrasound endoscopes in Chinese MIs need to be improved. In clinical practice, it is necessary to establish monitoring standards and detection criteria for duodenoscopes and linear array ultrasound endoscopes, so as to promote the effective implementation of endoscopy quality monitoring.