The academic thought of the physician in Qing Dynasty-Huang Yuanyu, is unique in history, but his thought is seldom used to guide acupuncture practice. This article clarified the relevance of Huang’s theory with acupuncture classics,as well as its guidance to the regulating qi and choosing acupoints in acupuncture clinical practice, so as to discuss his thought in acupuncture clinical application. Studies show that the application of Huang Yuanyu’s thought in acupuncture is prospective. It has improved the acupuncture treatment methods,and it may even have established a new mode of acupuncture treatment. Huang’s theory has promising prospect in clinical practice.