Abstract: By reviewing the original intention of constructing the syndrome differentiation system on the basis of thirteen pathogenesis， to emphasize that the pathogenesis is the key point for syndrome differentiation and treatment， which is the core of all TCM theories. Thirteen pathogenesis is established on the basis of nineteen pathogenesis in The Yellow Emperor's Inner Classic， and integrated the theory of important pathogenesis of later generations physicians. This paper puts forward a new syndrome differentiation system based on thirteen pathogenesis， which integrates the existing traditional dialectical methods， enriches and develops the theory system of pathogenesis of TCM.