Objective To observe the impacts of acupoint and nonacupoint on brain functional connectivity so as to explore the basis of function specificity of acupoint. Methods Twenty-one healthy volunteers were selected and randomized into acupoint group (12 cases) and nonacupoint group (9 cases). Acupuncture was applied to bilateral Zúsānlǐ (足三里 ST 36) and the site 3 to 4 mm lateral to Zúsānlǐ (足三里 ST 36) respectively on the subjects. Rotation needling technique was adopted. MRI was conducted before and 25 min after acupuncture respectively. Bilateral cingular gyrus was taken as seed point to analyze the situations of brain function connectivity in acupoint group and nonacupoint group.Results Brain functional connectivity presented extensively in either acupoint group or nonacupoint group. In comparison between acupoint group and nonacupoint group, in acupoint group, enhanced functional connectivity displayed in bilateral tonsillar, right cerebellar dentate nuclei, bilateral cerebellar uvula, left cerebellar declive, right cerebellar nodule, left inferior frontal gyrus, bilateral middle temporal gyrus, bilateral paracentral lobule, left cingular gyrus, right superior temporal gyrus, right anterior cingular gyrus and other regions, as well as posterior cingular gyrus. But brain connectivity in bilateral medial frontal gyrus, right inferior frontal gyrus, right cingular gyrus was weakened as compared with nonacupoint group. Conclusion The brain regions with functional connectivity induced are mostly same between acupoint and nonacupoint. But, the strength of brain functional connectivity in acupoint group is higher in overall than that in nonacupoint group.