To explore the neurophysiological mechanisms of acupuncture on Hegu(LI4) and Houxi(SI3) curing diseases and the functional specificity of them based on the technique of fMRI.Methods:Forty healthy right-handed volunteers，divided into Hegu(LI4) point group and Houxi(SI3) point group，20 cases in each group.The experiment took the modified block design.All healthy volunteers were stimulated at left Hegu(LI4) or Houxi(SI3)，acquiring the fMRI data with the same scanning sequences.All fMRI data were analyzed by AFNI program and the results were corrected with Monte Carlo method(P=0.002，α≤0.05).Results: 1) Many brain areas were actived with increased signal by stimulating at the left Hegu(LI4) which included：bilateral cerebellum，right thalamus and subthalamic nucleus，bilateral lentiform nucleus and putamen，right caudate，right cingulate gyrus，bilateral precentral gyrus，right posterior central gyrus，bilateral superior parietal lobule，right inferior parietal lobule，left inferior frontal gyrus，right middle frontal gyrus，right middle temporal gyrus，bilateral superior temporal gyrus，right supramarginal gyrus，left middle occipital gyrus，left insula. 2) As well as many brain areas were actived with increased signal by stimulating at the left Houxi(SI3) which included：bilateral cerebellum，left thalamus and ventral posterior medial，right caudate，right precentral gyrus，right middle frontal gyrus，left cingulate gyrus，bilateral insula. 3)It showed significant defferences between the Intergroup analysis results of stimulating at Hegu(LI4) vs Houxi(SI3)：the increased signal in left cingulated，precentral gyrus and decreased signal in right middle frontal gyrus，inferior frontal gyrus of Hegu(LI4) than Houxi(SI3).Conclusion:Present research directly illustrated the link of Hegu(LI4) with the face and mouth，as well as Houxi(SI3) with the neck and torso at the levels of central nervous system.And it also offered the objective neurophysiological evidence to the traditional Chinese medical theory-“fall and hand controlled by Hegu” and “Houxi associating with the governor vessel”.In addition，it explained the mechanism of Hegu treatment to hyperhidrosis，Houxi(SI3) treatment to neck lumbar diseases，and the analgesic function of both acupoints in some degree.Nevertheless，it provided the objective basis of functional specificity of the acupoints which were closed in location.