Meridian and collateral theory is the core of acupuncture theory. Simple using the syndrome differentiation system of internal medicine of TCM in clinical practice of acupuncture and moxibustion is difficult to reflect the core of acupuncture theories and characters of clinical acupuncture treatment. The establishment of clinical syndrome differentiation system of acupuncture should base on characters and laws of acupuncture and take the syndrome differentiation according to meridian and collateral theories as main body, syndrome differentiation according to location as key, syndrome differentiation according to eight principles as guidance, syndrome differentiation according to zang-fu theory as complementarity, and pay attention to application of acupoint specificity in clinic, so as to reflect unique character of acupuncture theory and insure the veracity of syndrome differentiation of acupuncture and efficacy of acupuncture treatment.