The overall development of the pharmaceutical industry has promoted the reconstruction of the traditional medical system, and the rapid popularization of modern medicines has brought new challenges and opportunities to natural medicine, such as traditional Chinese medicine (TCM). In this paper, the current problems in TCM promotion were analyzed, and the research focus and transformation trends of the future TCM were discussed from the perspective of the history of drug research. (1) The predicament of TCM promotion. First, in terms of drug research and development, TCM is a reverse verification from experience to theory, while modern medicine is a linear process of translating basic research into clinical application. Second, there is no direct connection among TCM registration, TCM supervision and mainstream international standards constructed by modern medicine. Third, TCM needs to face the scrutiny and judgment of Western thinking in global promotion due to the huge difference between Eastern and Western cultures. (2) Implications for modern pharmaceutical research and development. Traditional medicines have strong humanity, region and inheritance. Modern medicines have developed rapidly since the 19th century, and modern medicines (including chemicals and biological products) have gradually replaced traditional medicines and become the mainstream of the market. For example, aspirin, metformin and artemisinin are classic cases of traditional medicine being transformed into modern medicine. Traditional medicines are not confined to the characteristics of “crude, complex, vague”, and the discovery of modern medicines also shows the enlightenment or participation of traditional medicines. (3) Value regression for drug research and development. Humans form different races due to sociocultural symbols such as blood, regions, cultures, beliefs and customs. However, drugs have irreplaceable and important roles in health. Therefore, a set of extremely strict technical standards around effectiveness, safety and quality has been gradually formed in the modern new drug research and development, and the “cultural value” of drugs is required to transform into the “efficacy effect”. (4) The modernization of TCM. There are two main methods to develop new TCM medicines: Following the research and development mode of modern medicines, or following the research and development mode of traditional medicines. For the first method, within the framework of modern medicines, it is difficult for traditional medicines such as TCM to meet the research and development standards of modern medicines comprehensively. However, the existing difficulties do not mean denying the correctness of scientific standards. When the research and development mode of the traditional medicines is used, the efficacy of the new drug should withstand comprehensive reproducibility and examination, and understanding the material basis and exploring the mechanism of drug action are still the keys to clarifying and explaining TCM. In addition, the uniformity and stability of TCM quality are important components of drug management.