The systematic analysis of differential expression factors and biological mechanisms in acupuncture treatment at the level of gene expression regulation will help to clarify the specific pathophysiological characteristics of acupuncture, and it is possible to find new biological phenomenon and medical development clues from clinical effects of acupuncture. Therefore, it is necessary to select acupuncture treatment methods showing clinical efficacy, set up reasonable controls to identify differential expression factors with scientific and credible programs, and clarify the specific biological mechanism of acupuncture treatment. A comprehensive explanation of the mechanism based on the study of material basis of acupuncture effect will help to improve the clinical effect, guide the correct development of the subject and it may contribute to the clinic with the form of drug-active small molecules (acupuncture medicine) in the future.