Traditional Chinese Medicine (TCM) is characterized by regulating the integrity of the human body and has accumulated thousand-year experience in the use of Herb Formula (“Fu-Fang“ in Chinese) for managing complicated TCM Syndrome ( “ ZHENG ” in Chinese). In recent years, there has been increasing concern about the application of bioinformatics and systems biology approaches for deciphering the scientific basis and the systematic features of TCM. Based on the new trends in such an interdisciplinary field, which we termed TCM systems bioinformatics (TCMSB), we propose for the first time a map of “Phenotype network-Biological network-Herb network” with an attempt to uncover the network systems underlying, and identify network biomarkers for, TCM Syndrome and Herb Formula. This multilayer map can serve as a start point towards the systematic interpretation of TCM theory and practice, and give promise to bridge the gap between the ancient TCM and the coming systems biology-based medicine in both system and molecular levels. Moreover, TCMSB approaches, which combine the use of computational modeling and experimental studies, may not only help catch the traditional features of TCM in view of complex biological systems and lead to the step by step modernization for TCM, but may also educe new concept for the future integrative medicine and systems medicine.