Objective To investigate and intervene in a standard-exceeding event of microbial monitoring of pediatric ultrathin flexible bronchoscopes in a tertiary first-class maternity and child health care hospital, and to provide a basis for improving the cleaning and disinfection quality of flexible bronchoscopes and reducing healthcare-associated infection (HAI) caused by contamination of flexible bronchoscopes. Methods Flexible bronchoscopes with microbial contamination were recalled through contacting the manufacturer. The internal channels of the flexible bronchoscopes were examined using borescope, and leakage was tested. On-site sampling of the final rinse water system was conducted. The usage and disposal procedures of flexible bronchoscopes implemented by staff were investigated through on-site survey. Intervention measures were developed. Results The main problems were: 1 There were visible scratches and epidermal lifting on the tube surface of flexible bronchoscopes, with leakage testing indicating minor leakage. 2 Microbial detection of the final rinse water exceeded standards. 3 Some flexible bronchoscopes handling personnel lacked standardized pre-service training and assessment, leading to inadequate drying time and rough brushing of the bronchoscopes. In response to the existing problems, the manufacturer replaced the flexible bronchoscopes outer sheath and the filter for the rinse water generator, and installed a filter at the outlet of the final rinse water. After the hospital strengthened training, assessment, and supervision of the personnel handling flexible bronchoscopes, the re-inspection results were qualified. Conclusion The microbial count exceeding the standard for flexible bronchoscopes may be attributed to biofilm formation resulting from surface damage, contamination of final rinse water, and improper personnel handling. To prevent HAI related to flexible bronchoscopes, medical institutions should regularly inspect the lumens of in-use flexible bronchoscopes and test leakage, promptly repair those with significant damage. In addition, it is necessary to pay attention to the quality of rinse water, disinfection of water supply lines, as well as training and assessment of disposal personnel.