Objective To evaluate the microbial contamination levels of 10 kinds of Chinese herbal pieces,and explore the diversity of fungi and heat-resistant bacteria.Methods The total aerobic microbial count(TAMC),total yeast and mould count(TYMC),total heat-resistant microbial count(THRC)and 3 types control bacteria were detected according to the microbial limit inspection method of Chinese Pharmacopoeia 2020.Besides,the community characteristics of contaminated fungi and heat-resistant bacteria on prepared slices were analysed based on internal transcribed spacer(ITS)and 16S ribosomal DNA(16SrDNA)high-throughput sequencing method.Results The TAMC of 28％(14/50)samples exceeded 106 cfu/g,the TYMC of 20％(10/50)samples exceeded 104 cfu/g,the THRC of 68％(34/50)samples were higher than 10 cfu/g,and the bile-tolerant gram-negitive bacteria were detected in 40％(20/50)of the samples.Escherichia coli were found in 2 batches of the Pogostemon cablin,but Salmonella was not found in any sample.High throughput sequencing results showed that the fungi contaminated distributed in 12 phylums,777 genera and 1 467 species;the heat-resistant bacteria were mainly distributed in 5 phylums,57 genera and 74 species.The decoction pieces contained Aspergillus flavus and heat-resistant pathogens such as Bacillus amyloliquefaciens,Staphylococcus lentus,and Staphylococcus warneri.Conclusion The 10 kinds of decoction pieces are generally contaminated by microorganisms,and some of them contain toxic fungi and pathogenic heat-resistant bacteria,which poses a potential risk of microbial pathogenicity for patients.