Traditional Chinese medicines (TCMs) have a long history of playing a vital role in disease prevention, symptom alleviation, and health improvement. However, their complex ingredients and as-yet-unknown mechanisms restrict their application. With increasing evidence indicating that the gut microbiota is important in host health and may be associated with the therapeutic activity of TCM components, it may now be possible to assess the effects of TCMs from the perspective of the gut microbiota. The gut microbiota functions within four major physiological pathways as follows: It participates in host metabolism, forms global immunity, maintains homeostasis of the gastrointestinal tract, and affects brain function and host behavior. This article reviews the reported correlations between TCMs and certain diseases, such as chronic liver disease, ulcerative colitis, obesity, and type 2 diabetes, and elucidates the underlying mechanisms, with a focus on changes in the gut microbiota. In future, further studies are required with more advanced experimental design in order to reveal the interactions between TCMs and the gut microbiota, and provide new insight into and guidance for TCM-based drug discovery.