Abstract: Treatment mechanism of Shenmen acupoint from the perspective of the complex network was explored, which would provide experimental references for magnetic stimulation therapy. The brain functional network differences between the magnetic stimulation at Shenmen acupoint and resting state of nine healthy volunteers were studied by analyzing the network features. The correlation coefficients under magnetic stimulation at Shenmen acupoint are lower than those at resting state. Comparing to the resting state, average clustering coefficient, average shortest path length and average degree change significantly. The small world attribution was enhanced. Magnetic stimulation at Shenmen acupoint reduces the compact degree between the nodes and makes the connection much looser. Synchronization capability of network becomes weak. The efficiency reduces and the network size can be diminished. Then the brain is likely to be in a state of comparative calm and conduces to sleeping.