The clinical progress of traditional Chinese medicine (TCM) in history was closely related to the high incidence of epidemic diseases. At the end of Han dynasty and in Wei and Jin dynasties, On Cold Damage was written. During Jin and Yuan dynasties, there were fire-heat theory and On Spleen and Stomach due to epidemic diseases. During Ming and Qing dynasties, the school of warm diseases emerged after the completion of the book On Plague Diseases. In the process of changing and development of epidemic diseases, TCM formed basic methods of syndrome differentiation and treatment and the system of clinical diagnosis and treatment. TCM clinical progress has never stopped.