Endophytes refer to a group of microorganisms that coexist with healthy plant tissues and organs at a certain or all stages of their life cycle, but do not cause obvious disease characteristics in the host plant, including endophytes and fungi. Medicinal plants contain abundant endophytic bacteria, which are closely related to the growth and development of drugs, metabolic activities, and the production of active medicinal ingredients, and also directly affect the authenticity indicators of drugs. Gastrodia elata Bl., Scutellaria baicalensis Georgi, Bupleurum chinense DC., Polygonatum sibiricum Red., Cistanche deserticola Y.C.Ma, and other traditional Chinese medicinal herbs are commonly used in traditional Chinese medicine for prevention, treatment, and diagnosis of diseases. In recent years, with the proposal of the "Healthy China" strategy and the increasing emphasis on traditional Chinese medicine resources, research on the microbiome of medicinal plants has been increasing. In order to collect and integrate numerous research results on endophytic fungi in plants and form a knowledge system to promote comparative research, literature screening and information extraction analysis were conducted, and a knowledge base II of medicinal plant microbiome was constructed for research on quality monitoring and authentic evaluation of medicinal plants. The database covers the names, host plants, classifications, genera, families, orders, classes, phyla, functions/biological effects, techniques, sequence lengths, NCBI reference sequence numbers/GenBank, references, and corresponding links of medicinal plant microorganisms. This system supports querying the microbiome related content of five medicinal plants, including Gastrodia elata Bl., Scutellaria baicalensis Georgi, Bupleurum chinense DC., Polygonatum sibiricum Red., Cistanche deserticola Y.C.Ma. Therefore, this database will help provide background support and reference value for research related to the microbiome of medicinal plants, and provide reference for the future creation of relevant drug quality testing standards and new methods for evaluating the authenticity of medicinal materials.