Based on the description of epidemic diseases in the chapter of “The Story of Bian Que” in Records of Historian, the author has analyzed and explored the truthfulness of its background data and the possibility of the plague spreading at that time from both macro and micro angles. The symptoms of plague including chills and fever, the digestive symptoms and the symptoms in central nerve system made great influence on the formation of some doctrines in traditional Chinese medicine (TCM) such as exopathic heat disease doctrine, internal injury of spleen and stomach doctrine and epidemic febrile disease doctrine. The course of exogenous febrile disease was similar to that of the plague, thus the theory of six meridians was formed. According to above phenomena, the author has explored the effect on the initial medical theory, primitive religion and culture due to the spreading of epidemic diseases from the angles of epidemiology, the theory of images and figures, complicated thought ways depending, as well as archaeological studies. Then the hypothesis of medicine originated from epidemic diseases was proposed. The author also put forward some opinions on the relationship between epidemic diseases spreading and traditional education of TCM, sustained development of TCM education, as well as the integration of TCM and WM.