Abstract: With the significant changes of clinical problems faced by traditional Chinese medicine， we should attach importance to new theoretical innovation on the basis of inheritance and clinical practice. The formation of syndrome differentiation system originates from Treatise on Febrile Diseases written by Zhang Zhongjing. Although different methods of syndrome differentiation have their own applicable scopes and characteristics， the generality of them lies in grasping the pathogenesis. Professor Zhou Zhongying believes that pathogenesis analysis should be put on the top priority for syndrome differentiation. A new system of syndrome differentiation and treatment should be constructed with pathogenesis as the core and multiple syndrome differentiation as a whole， so as to refine a more practical， flexible and comprehensive method for syndrome differentiation， which will not only activate the syndrome differentiation， but also make it easier to master. The basic elements of syndrome differentiation concerning pathogenesis include pathological factors， nature of disease， location of disease and condition of disease， all constituting the syndrome factors of diagnosis of syndrome differentiation. We should grasp the structure of pathogenesis in the application of syndrome differentiation of pathogenesis， clarify the complexity of compound pathogenesis and distinguish the identity of pathogenesis from its difference. The diagnosis and treatment scheme should be made with disease pathogenesis as the main part in syndrome differentiation of pathogenesis. And the syndrome elements should be taken as the contents， which contain syndrome differentiation， nature of disease， location of disease， condition of disease， evolution of disease as well as its treatment， prescription samples， modification and clinical essentials.