There are abundant endophytic bacteria, fungus and actinomycete in medicinal plants. The microorganisms of medicinal plants are closely related to the growth, reproduction and metabolic activities of medicinal plants, which can not only affect the formation and content of medicinal ingredients in plants, but also affect the geoherbalism of Chinese medicinal materials. Angelica sinensis, Astragali Radix, Rheum palmatum L., Codonopsis pilosula and Glycyrrhiza uralensis Fisch are five traditional and authentic medicinal materials in Gansu Province, which are also important sources of TCM clinical drugs. In recent years, more and more studies have been made on the microbiome of these five medicinal plants in Gansu. In order to integrate data resources and results of numerous studies and promote comparative studies, literature review and information extraction analysis were carried out, thereby constructing a knowledge base for Gansu medicinal plant microbiome to assist research on the quality and geoherbalism of Gansu medicinal plants. The database includes species name, host plant, classification, genus, family, order, class, phylum, function, technique, sequence length, NCBI reference serial number/GenBank, references and corresponding links. This interface supports the query function for the contents of the microbiome of the above medicinal plants. Therefore, this database will help to provide research basis for the development and utilization of medicinal plant microbiome in Gansu, and provide reference for the establishment of a new method for quality control and geoherbalism evaluation of medicinal plants in Gansu.