Abstract: OBJECTIVE To explore the relationship between microbial contamination and varieties, medicinal parts and processing methods of Chinese herbal decoction pieces.METHODS Total aerobic count, total mold and yeast count were carried out according to the method of Chinese Pharmacopoeia. SNK test was used to analyze the data. Biochemical analysis and ABI 3500 gene sequencing were used to identify thermophilic bacteria in Chinese herbal pieces.RESULTS The analysis of lg values of aerobic bacteria counts, mold and yeast count showed that there were significant differences among different varieties, different medicinal parts and different processing methods of Chinese meteria medica decoction pieces. The varieties of Genkwa Flos and Albiziae Cortex, the medicinal parts of flowers, the processing method of net processing showed the greatest bacterial contamination. After 30 min of 100℃ water bath, the thermophilic bacteria could be basically removed from the Chinese meteria medica decoction pieces, but thermophilic bacteria could still be identified from Ophiopogonis Radix and Genkwa Flos.CONCLUSION The differences of varieties, medicinal parts and processing methods of Chinese materia medica decoction pieces are closely related to microbial contamination. After decocting, Ophiopogonis Radix and Genkwa Flos still can not completely kill thermophilic bacteria.