Abstract: OBJECTIVE To investigate 11 kinds of Chinese herbal medicine(CHM) microorganism contamination and assess potential risk, and establish the microorganism database of Chinese herbal medicine. METHODS The gene microarray technology was used to describe microbiome communities in 11 kinds of Chinese herbal medicines. RESULTS A total of 174 species of microorganism were identified, which consisted of bacteria, fungi, and virus. Bacteria was the most dominant fraction, which accounted for 75.29% of total microorganism. The microorganism database of CHM was initially established by sorting and analyzing of the detection results of 174 species of microorganisms. The detection rate for Salmonella enterica, Yersinia spp., and Shigella spp. were 45.45% (5/11), 45.45% (5/11), and 36.36% (4/11), respectively. Several opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae and Pseudomonas aeruginosa were also detected. The detection rates were 63.63%(7/11), 45.45%(5/11), 45.45%(5/11), and 9.09%(1/11), respectively. CONCLUSION This study shows that CHM is contaminated by some microorganisms. Further research on risk assessment and microorganism database of CHM should be carried out to provide traceability analysis of pathogens so as to ensure the safety and efficacy of CHM.