Metabonomics is a newly emerging modern technology in the Post-genome era and has been being used widely in the study on modern Chinese medicine. But it have been rarely used in the study on acupuncture therapy. In the present paper, the authors introduce the unique advantages of metabonomics in the systemtic biology and its widespread studying basis in the field of modern Chinese medicine. Metabonomics and Chinese medicine including acupuncturology are of some similar characteristics such as entirety, comprehensiveness and dynamic changes. Moreover, the authors make a primary discussion and strategic analysis on the key issues of researches about sham acupuncture, chrono-acupuncture, mechanisms of acu-moxibustion underlying improvement of clinical severe disorders and various indications problems, regularities of combination of acupoints in different recipes, etc. by using metabonomics.