Comparative effectiveness research (CER) has gained more and more popularity, which brought great response in the USA and other developed Western countries. There is no doubt that CER is a new idea and a milestone in health care research. CER is also known as "patient-centered outcomes research", which means patient is the core element in the whole system of CER. Chinese medicine could make new achievements and further development by introducing CER into clinical research. This article mainly introduced the background, features and contents of CER and summarized how to conduct CER in Chinese medicine by referring to some published literature in order to enlighten Chinese medicine researchers.