Abstract:[Background] A large amount of Chinese medicine residues is produced every year in China, which not only wastes medicinal materials but also causes environmental pollution. Semipermeable membrane aerobic composting of Chinese medicine residues is an effective method to address the solid waste and realize the regeneration value and sustainable development of Chinese medicine waste resources. [Objective] To explore the composting process and the suitable C/N ratio of Chinese medicine residues for fermentation, and reveal the relationship between functional microorganisms and composting process based on the changes of microbial community structure during the composting process. [Methods] Chinese medicine residues were composted with cow dung as the auxiliary materials, and the 16S rRNA gene high-through sequencing was employed to disclose the succession of microbial community structure during the composting process. The temperature, C/N ratio, moisture content, pH, NH4+-N, total nutrients, and seed germination index were measured, and their relationship with the changes of functional microorganisms was explored. Furthermore, the Chinese medicine residue fertilizer was applied to the seeds of the medicinal plants Isatis indigotica and dandelion, and the seed germination was examined to verify the performance and safety of the fertilizer. [Results] The high-temperature period of Chinese medicine residue composting with a C/N ratio of 25 exceeded 7 days. With the extension of fermentation time, the moisture content significantly decreased and the pH gradually increased. The obtained fertilizer showed the NH4+-N content of 78.8 mg/kg (<400 mg/kg), total nutrient content of 5.48% (>5%), and the germination index (GI) reaching 161.34%, which met the standards of organic fertilizer fermentation. The composting performance of Chinese medicine residues with the C/N ratio of 25 was better than that with the C/N ratios of 20, 30, and 35. During the high-temperature fermentation of the pile, Lysinibacillus and unclassified_f__Rhizobiaceae were the dominant bacteria and Mycothermus and Aspergillus were the dominant fungi. Moreover, the obtained fertilizer promoted the seed germination of I. indigotica and dandelion. [Conclusion] The results of this study not only provide a theoretical basis for further research on the mechanism of microbial compost and different types of Chinese medicine residue compost, but also provide a reference for solving the problem of effective resource utilization of Chinese medicine waste, and expand the application of semi-permeable membrane aerobic compost process in the field of environmental pollution control.