Objective To understand the distribution and changing trend of multidrug-resistant organisms (MDROs) from clinical specimens in traditional Chinese medicine hospitals, provide scientific basis for rational clinical antimicrobial use. Methods In vitro antimicrobial susceptibility testing data of frequently clinically isolated bacteria from traditional Chinese medicine hospitals nationwide from 2018 to 2021 were collected. In vitro antimicrobial susceptibility testing methods included disk diffusion method, automated apparatus method, and E-test method. Antimicrobial susceptibility testing results were interpreted according to the American Clinical and Laboratory Standards Institute (CLSI) standards. According to the technical program of China Antimicrobial Resistance Surveillance System (CARSS), the distribution of bacterial species as well as the detection and changing trend of MDROs were analyzed with WHONET 5.6 software. Results Among clinical isolates from 2018 to 2021, Gram-positive and Gram-negative bacteria accounted for 26.4%-27.4% and 72.6%-73.6%, respectively, with a stable trend. Among Gram-positive bacteria, isolation rates of methicillin-resistant Staphylococcus aureus (MRSA) increased from 28.5% to 30.2%, however, methicillin-resistant coagulase negative Staphylococcus (MRCNS), vancomycin-resistant Enterococcus faecium and penicillin-resistant Streptococcus pneumoniae (PRSP) all showed decreasing trends, from 76.1%, 2.7% and 3.1% in 2018 to 72.4%, 1.5% and 1.8%, respectively. Among Gram-negative bacteria, isolation rates of carbapenem-resistant Escherichia coli and carbapenem-resistant Klebsiella pneumoniae gradually increased from 1.6% and 10.4% to 1.9% and 13.3%, respectively. However, isolation rates of carbapenem-resistant Pseudomonas aeruginosa and carbapenem-resistant Acinetobacter baumannii showed downward trends, decreasing from 22.4% and 49.5% to 21.9% and 48.2%, respectively. In addition, detection of MDROs varied significantly in different regions. Isolation rates of MRSA were highest in Anhui, Jiangsu, and Guangdong Provinces, but lowest in Yunnan, Heilongjiang, and Jilin Provinces. Meanwhile, isolation rates of carbapenem-resistant Klebsiella pneumoniae were highest in Anhui Province, Shanghai City, and Henan Province, but lowest in Ningxia, Qinghai and Jilin Provinces. Conclusion The isolation rates of MRSA, carbapenem-resistant Klebsiella pneumoniae, and carbapenem-resistant Escherichia coli show increasing trends, while isolation rates of other clinically isolated MDROs present downward trends or remain unchanged. There are temporal and regional differences in the isolation rate of MDROs. Management of rational use of antimicrobial agents as well as healthcare-associated infection prevention and control should continue to be strengthened, bacterial antimicrobial resistance monitoring should be conducted well.