Starting from the occurring regularity of Traditional Chinese Medicine(TCM) syndrome, the topological structure of TCM syndromes was discovered and then the methodology of topology studying TCM syndrome was formed. This methodology has the advantage of realizing the analysis and operation on the basis of information intact of TCM syndrome, so as to achieve correspondence of the nature and disease evolution of topology analysis results. Topological methods can break out the complex structure of the scientific connotation of TCM syndromes, build up the criteria of diagnosis of syndromes, form the new method of syndrome differentiation of the “four characteristics and five stages”,and provide a theoretical basis for the biological basis of syndromes; it can explain precisely corresponding rules of syndrome-principle-method-recipe -medicines; it can establish the system of visualization on the process of the treatment according to syndrome differentiation, forming the evaluating system of level of treatment according to syndrome differentiation; it can rebuild the basic structure of TCM diagnosis and treatment, interprete the archetypes of TCM diagnosis and treatment system, to establish the evaluation system of TCM clinical efficacy. With the crack and interpretation of complex structure of TCM syndrome, finding the basis of the theory of TCM syndrome of mathematical science and making the syndromes of TCM theory and modern science are the combination of dialogue and communication, and there is hope to open the new era of development of TCM theory and clinical practice.