Carbon dots (CDs) are novel zero-dimensional spherical nanoparticles with water solubility, biocompatibility and photoluminescence properties. As the variety of raw materials for CDs synthesis becomes more and more abundant, people tend to choose precursors from nature. Many recent studies have shown that CDs can inherit properties similar to their carbon sources. Chinese herbal medicine has a variety of therapeutic effects to many diseases. In recent years, many literatures have chosen herbal medicine as raw materials, however, how the properties of raw materials affect CDs has not been systematically summarized. The intrinsic bioactivity and potential pharmacological effects of CDs have not received sufficient attention and have become a 'blind spot' for research. In this paper, the main synthesis methods were introduced and the effects of carbon sources from different herbal medicine on the properties of CDs and related applications were reviewed. In addition, we briefly review some of the biosafety assessments of CDs, and make recommendations for biomedical applications. CDs that inherit the therapeutic properties of herbs can enable diagnosis and treatment of clinical diseases, bioimaging, and biosensing in the future.