The importance of evidence-based medicine (EBM) in clinical acupuncture-moxibustion research is discussed in the paper. The application of EBM and problems in clinical acupuncture-moxibustion research are reviewed. It is put forward that thinking and assumptions of the combination of the evaluation of clinical effectiveness and EBM. The characteristics of acupuncture-moxibustion theory determine that the design of clinical research of acupuncture cannot completely apply the methods of EBM. Future efforts should be made to explore the integrated research design which is adhering to the guidelines of clinical practice of acupuncture. The features and advantages of traditional therapeutic practices should be preserved, and the advanced methods in EBM should be applied. It is great to improve the reliability and repeatability of clinical acupuncture-moxibustion research and to improve the standard and the evaluation system of clinical acupuncture.