The research of traditional Chinese medicine clinical represented by the randomized controlled trial (RCT) has developed rapidly, But it also revealed two problem. The "combination between disease and syndrome" reflects the common law of disease and the patient's personality characteristics, and individual therapy focuses on dynamic effect which is more suitable for research environment in the real world the Institute of Medicine of the US National Academy of Science proposed the comparative effectiveness research (CER) to compare the research and analysis of different treatment methods. Building clinical research methods in the real world needs to carry on innovative exploration, and studies the methods and specifications of clinical research in the real world from the elements of clinical design, the control of bias, data management, statistical analysis, ethics and other clinical researches. On the basis, the comparative effectiveness research of "real world" and the "combination between disease and syndrome" needs to be carried out. The comparative effectiveness research of traditional Chinese medicine in the real world includes retrospective and prospective studies. The retrospective study is to analyze and compare based on historical data to provide clues and evidence for prospective study. The prospective study is to build follow-up platform for patients to carry on prospective study design. © 2012 IEEE.