As technologies used to study the gut microbiota have improved, the relationship between the gut microbiota and health has become increasingly obvious. Herbal medicines have been used for thousands of years, and are known to be “simple, convenient, cheap, and effective”. However, due to many factors, such as their complex composition, unclear active compounds, and poor knowledge of their underlying mechanisms, the clinical applications of herbal medicines are not widely recognized. Recently, there have been an increasing number of studies which have investigated the interaction between the gut microbiota and herbal medicines. We have found that interactions between the gut microbiota and herbal medicines occur primarily through two pathways. One pathway is that the gut microbiota “digests” the herbal medicines into absorbable active small molecules, which enter the body and induce physiological changes. The other is that herbal medicines regulate the composition of the gut microbiota and its secretions, thereby changed gut microbiota and its secretions inducing physiological changes. In summary, the interactions between the gut microbiota and herbal medicines can be attributed to absorbable active small molecules and changed gut microbiota and its secretions. Our findings will aid the exploration of the mechanisms and pathways underlying the function of herbal medicines in the future. This review also summarizes the direction of future research and the main problems faced by the current researchers.