Abstract: The pharmacodynamic substance of traditional Chinese medicine (TCM) is an important basis for its mechanism and quality control, and also a key scientific issue for the inheritance and development of TCM. However, the complex characteristics of multi-component, multi-target and integrity of TCM, as well as the limitations of modern scientific research technical methods, have brought great challenges to the research. The interactions between Chinese medicine and intestinal flora provide us with a new idea. Based on the effective role of TCM and the hypothesis of correlation between intestinal flora and disease, the research on the material basis and mechanism of action of TCM based on intestinal metabolomics mostly explored the relationship between microflora and host phenotype, gradually deepening, and finally focused on the relationship between intestinal strains and molecular levels. This paper summarized the research ideas and key technologies of this model, in order to provide reference for the application of this model.