In recent years, clinical research in traditional Chinese medicine (TCM) has witnessed vigorous development, with increasingly close integration with clinical epidemiological methodologies. However, certain controversies persist, such as the difficulty in aligning epidemiology’s population-based perspective with TCM’s principle of syndrome differentiation and treatment and the characteristics of individualized diagnosis and treatment. This paper reviews the development and current status of TCM clinical research, integrating the practice rules of TCM, and analyzes the manifestations and applicability of the basic characteristics of epidemiology in TCM clinical research. The study shows that epidemiological concepts and characteristics are fully compatible with the practical features of TCM clinical practice and its research needs. Moreover, epidemiological techniques can effectively uncover and elucidate the scientific basis of TCM clinical practice. Building on these analyses, we propose future directions for TCM clinical research, aiming to promote the integration of epidemiology and TCM clinical research and advance TCM clinical research to a higher level.