Objective To investigate the pollution status of ultrasonic atomization fumigation and washing machine of traditional Chinese medicine and the effect of precision disinfection intervention, and to provide scientific basis for strengthening the cleaning and disinfection work of ultrasonic atomization fumigation and washing machine of traditional Chinese medicine. Methods From January to February 2024, samples were collected from the surface of seven ultrasonic atomization fumigation and washing machines of traditional Chinese medicine that could be used normally in the Department of Traditional Chinese Proctology of the First People’s Hospital of Longquanyi District, Chengdu. Samples were collected from four points, namely the nozzle, the front edge of the hip bath cover, the rear edge of the hip bath cover, and the outer edge of the hip bath cover, and at four times, namely before use, after use, after pre-intervention routine disinfection, and after post-intervention precision disinfection (including training of personnel, solidification of disinfection process, and improvement of disinfection supplies), to compare the pollution status and disinfection effect of the object surface at different points and sampling times, and analyze the microbial detection. Results In terms of different times, the qualified rate of specimens was 28.6% before use, which decreased to 14.3% after use; the qualified rate of specimens was 39.3% after pre-intervention routine disinfection, which increased to 92.9% after post-intervention precision disinfection, with a statistically significant difference (χ2=17.923, P<0.001). A total of 158 strains of bacteria were detected from unqualified specimens, including 121 strains of Gram-positive bacteria (accounting for 76.58%) and 37 strains of Gram-negative bacteria (accounting for 23.42%). The detected bacteria were mainly common environmental bacteria. The top three were Kocuria rhizophila, Dermacoccus nishinomurai, and Microbacterium aureum. The main pathogenic bacteria of common nosocomial infections were Staphylococcus epidermidis and Escherichia coli, and no multi-drug resistant strains were detected. Conclusion Targeted cleaning and disinfection measures should be taken to ensure the disinfection effect and reduce the risk of nosocomial infection for special medical instruments such as ultrasonic atomization fumigation and washing machine of traditional Chinese medicine.