This paper analyzed the theoretical structure of Chen Shiduo’s theory of organ manifestations from its basic theory, composition and application. It can be concluded that Chen theory was highly influenced by Taiji Tushuo, and it provides a new theory of organ manifestations, which is “life-gate——water and fire”. By putting forward a new generation-restriction relationship, it forms a theory which surrounded liver. Moreover, it offers new methods in the diagnosis and treatment of liver deficiency, which is “tonifying kidney water” and “tonyfying liver water”. Therefore, Chen’s theory could be seen as a revolution under the impact of philosophy of Song and Ming dynasties. This paper will further assist in the research of Chen Shiduo theories, theory of organ manifestations past and present, and TCM theories regarding liver.