Abstract: This paper expounds the construction process， innovation and significance of Professor Zhou Zhong-ying's pathogenesis differentiation system， and discusses the concept of pathogenesis and its relationship with syndrome. It is believed that the highest realm of TCM syndrome differentiation is applying the theory flexibly， and understanding the pathogenesis is the understanding of the essence of the disease. Pathogenesis is the definition of the nature of disease， while syndrome is the summarization of pathogenesis. Both of them are characterized by variability and regularity. The pathogenesis differentiation system not only embodies the clinical characteristics of pathogenesis changing in accordance with syndrome， but also presents the flexibility of syndrome differentiation. It also puts forward that future pathogenesis research can be designed from different aspects and levels， in order to guide clinical practice.