Acupuncture is an important treatment of traditional Chinese medicine (TCM) by mechanically stimulating specific acupoints with fine needles, which can be used for treatment of neurodegenerative diseases (e.g. Parkinson’s disease, PD; Alzheimer’s disease, AD; Huntington’s disease, HD). Despite its well-documented efficacy, its biological basis remains largely elusive. Recent studies showed that acupuncture can up-regulate the autophagy level to promote the clearance of aggregated proteins, which can relieve symptoms of neurodegenerative diseases. Autophagy is the orchestrated bulk degradation of damaged organells, misfolded or aggregated proteins. It is an intracellular recycling system that functions during basal conditions in organelle and protein quality control. Loss of basal autophagy in the central nervous system is closely related to age-related neurodegeneration as seen PD, AD, HD. This paper summarized the studies on the regulating effect of acupuncture on the autophagy level in neurodegenerative diseases, and provided perspective for elucidating the molecular mechanism of acupuncture.