Ample clinical reports and neuroimaging studies have demonstrated that the acupuncture has sustained effects after manipulation. However, most previous fMRI studies of acupuncture have paid little attention to this issue, only investigating on the manipulation effects. In the current study, we attempted to explore both acupuncture effects, which have positive influence to therapeutic efficiency, to reveal the neural mechanism of acupuncture. This paper combined the conventional general linear model (GLM) and independent component analysis (ICA) to study the topography and the temporal feature of brain activity to detect the brain responses to stimulation at ST36 (Zusanli) and a sham acupoint. The results showed that the manipulation-related effects and the sustained acupuncture effects separately induced statistically significant increases/decreases in the cortical-subcortical areas, including the anterior cingulate cortex (ACC), ventrolateral prefrontal cortex (VLPFC), supplementary motor area (SMA) primary/secondary somatosensory cortex (SI/SII), occipital cortices and midbrain. Our findings suggested that the analgesia effects of ST36 integrated sophisticated physiological and psychological procedures. In addition, our results have shed light on methodology in acupuncture research.