The javascript:void(0)manipulation and sustained effects of acupuncture have been investigated in multiple studies, but several findings are inconsistent with one another. One possible explanation for these discrepancies is that different modalities of acupuncture were utilized in these studies. In the present study, we investigated both the manipulation and sustained effects of acupuncture in different modalities, including manual acupuncture (MA), electroacupuncture (EA) and transcutaneous electrical acupoint stimulation (TEAS). MA, EA, TEAS and sensory control stimulation were applied to 18 healthy subjects, and combined block-designed and resting-state fMRI scans were performed. In analyzing these data, the block-designed datasets were used to assess the manipulation effect by employing a modified general linear model. The data from the resting states, before and after stimulation, were used to explore the brain networks involved in the sustained effect. The results showed that the two 1-min stimulation periods produced similar activation patterns in the sensory control with positive activation in the sensorimotor areas and negative activation in the default mode areas. Although similar patterns could be detected in the first stimulation period in MA, EA and TEAS, no positive activation result was observed in the second stimulation period, and EA showed a more extensive deactivation compared to MA and TEAS. Additionally, all three of the modalities of acupuncture stimulation could increase the instinct brain network in rest. A more secure and spatially extended connectivity of the default mode network was observed following MA and EA, and TEAS specifically increased the functional connectivity in the sensorimotor network. The present study suggested that different brain mechanisms might be recruited in different acupuncture modalities. In addition, the findings from our work could provide methodological information for further research into the mechanism of acupuncture.