From the perspectives of big culture, big science, and big medicine, this article traced back to the root, and analyzed the cultural background, philosophical foundation, and medical practice of the concept of the five internal organs of the TCM from Huangdi Neijing. It is believed that the five internal organs are ancient people who use internal organs as an object image to generate functional concepts “class concepts” through imagery thinking, and under the guidance of the concept of unity between man and nature, they incorporate it in the “four-seasons rule”, thus forming the concept system of the five internal organs with the core connotation of growing collection, the logical method of essential qi-yin and yang-five elements. At the same time, the formation of the concept also experienced a process of interaction and mutual recognition between theory and practice. In addition, this article also discussed the scientific significance of the concept of five internal organs, and pointed out that the five internal organs of the TCM were a structural functional concept. It is the product of the Chinese system thinking. In the development of science and technology to the comprehensive stage, the TCM theories including the concept of five internal organs have certain advantages in the theoretical scientific significance and medical practice, for the development of life sciences and medical sciences.