With the continuous progress of biomedical technology, biomaterial coatings play an important role in improving the performance of medical devices and promoting tissue repair and regeneration. The application of natural medicine to biological materials has become a hot topic due to its diverse biological activity, low toxicity, and wide range of sources. This article introduces the definition and classification of natural medicines, lists some common natural medicines, such as curcumin, allicin, chitosan, tea polyphenols, etc., and lists some biological activities of some common natural medicines, such as antibacterial, antioxidant, antitumor, and other properties. According to the different characteristics of natural medicines, physical adsorption, chemical grafting, layer-by-layer self-assembly, sol–gel and other methods are combined with biomaterials, which can be used for orthopedic implants, cardiovascular and cerebrovascular stents, wound dressings, drug delivery systems, etc., to exert their biological activity. For example, improving antibacterial properties, promoting tissue regeneration, and improving biocompatibility promote the development of medical health. Although the development of biomaterials has been greatly expanded, it still faces some major challenges, such as whether the combination between the coating and the substrate is firm, whether the drug load is released sustainably, whether the dynamic balance will be disrupted, and so on; a series of problems affects the application of natural drugs in biomaterial coatings. In view of these problems, this paper summarizes some suggestions by evaluating the literature, such as optimizing the binding method and release system; carrying out more clinical application research; carrying out multidisciplinary cooperation; broadening the application of natural medicine in biomaterial coatings; and developing safer, more effective and multi-functional natural medicine coatings through continuous research and innovation, so as to contribute to the development of the biomedical field.