We tested whether the stimulation of acupoints in the same spinal segments could induce different central responses with functional magnetic resonance imaging (fMRI) study. Stimulation of acupoints ST36/SP6 (Zusanli/Sanyinjiao) or GB34/BL57 (Yanglingquan/Chengshan) both activated primary and secondary somatosensory area, insula, ventral thalamus, parietal Brodmann Area 40, temporal lobe, putamen, and cerebellum, while de-activated amygdala. Nevertheless, ST36/SP6 stimulation specifically activated orbital frontal cortex and de-activated hippocampus. Alternatively, stimulation of GB34/BL57 activated dorsal thalamus and inhibited those of primary motor area and premotor cortex. Thus, stimulation of acupoints in the same spinal segments induced distinct though overlapped cerebral response patterns, which indicated the existence of acupoint specificity.