Intestinal flora associated with a variety of organs may reflect the holistic view of traditional Chinese medicine(TCM).Intestinal flora has been concerned in a wide range of studies involving the mechanism，compatibility，and toxicology of Chinese medicines.Chinese medicines can regulate the number and composition and improve the abundance and diversity of intestinal flora.Moreover，intestinal flora can metabolize and transform the active ingredients in Chinese medicines to improve the efficacy of Chinese medicines.Multi-omics including metabolomics can help to fully explain the interaction mechanisms between intestinal flora and Chinese medicines through multi-level analysis.We reviewed the relevant articles published in the last decade to explain the interactions between intestinal flora and Chinese medicines.The progress in the research on intestinal flora in the fields of efficacy，compatibility，processing，and toxicology of Chinese medicines and the application of multi-omics was summarized.This review aims to provide a theoretical basis for further research on the relationship between intestinal flora and Chinese medicine and the application of multi-omics in this research field.