With the modernization and globalization of acupuncture and moxibustion, scientifically explaining the classical theory of acupuncture and moxibustion becomes one of the focus of the traditional medicine researches. Metabonomics is an important method of systematic biology and has been widely applied in many fields. Recently, it is an inevitable trend to combine acupuncture and moxibustion and metabonomics to investigating the mechanism of acupuncture. In this review, we summarized the advanced detecting methods of metabonomics, the analysis strategies and software of metabonomics and its current application status in the key scientific problems of acupuncture and moxibustion. In conclusion, we believe that metabonomic method will bring new directions for acupuncture research as well as clinic practice, in supportive of its modernization and globalization.