Comparative effectiveness research (CER) iscurrently a very popular new research modality in the field of international health care reform，and it is gradually known by domestic researchers.At the same time，its “patient-centered” philosophy is consistent withthe “holistic medicine” of Traditional Chinese Medicine (TCM).Hence，how to apply the CER in TCM which regards“holistic medicine” as the core concept is a significant issue.We summarized and concluded themethodological core of CER and the “holistic medicine” philosophy of TCM.Meanwhile we listed relevant examples and discussed the application of CER in the field of TCM which regards “holistic medicine” as the core concept.By summarizingthe key points in design of CER study，we can provide reference for future researchers to conduct similar study.