With the recognition of the important role of gut microbiota in both health and disease progression, attempts to modulate its composition, as well as its co-metabolism with the organism, have attracted special attention. Abundant studies have demonstrated that dysfunction or imbalance of gut microbiota is closely related to disease progression, including endocrine diseases, neurodegenerative diseases, tumors, cardiovascular diseases, etc. Herbal medicines have been applied to prevent and treat diseases worldwide for hundreds of years. Although the underlying mechanism seems to be complex, one of the important ones is through modulating gut microbiota. In this review, co-metabolism between herbal medicines and microbiota, as well as the potential pathways are summarized from most recent published papers.