Interactions between the components of traditional Chinese medicine (TCM) and the intestinal microenvironment are a key to TCM effectiveness.Studies investigating the complex relationship among TCM components, intestinal microenvironment, and enterocytes are vital for elucidating the effective substances of TCM and the mechanisms underlying their activities.With the development of theories and techniques across multiple disciplines, particularly the emergence of herb genomics, investigation into the interactions between TCM components and intestinal microenvironment has evolved from the biotransformation of components and regulation of flora structure and immunity into a study at the gene level, which involves structural and functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, and metagenomics.This review summarizes the research progress in terms of the scope of TCM and proposes areas for future studies.