Abstract：Study on the changes of brain functional connections during acupoint magnetic stimulation based on the complex network theory. Using crosscorrelation and mutual information method, the channel relationships of EEG signals of seven subjects were analyzed before, during and after magnetic stimulation on acupoint and the corresponding brain functional networks were constructed. The centralization indices were calculated using complex network analysis method and then the key brain regions of each stimulation mode were obtained. The results showed that comparing with the functional network before stimulation, the relationships between the nodes of parietal lobe and central region were unified enhanced during 1 Hz stimulation, meanwhile, the relationships among the nodes of frontal lobe, occipital lobe and top occipital lobe were unified weakened. However, the unified enhanced area during 3 Hz stimulation concentrated among the nodes of frontal lobe, central region, parietal lobe and temporal lobe. Nodes with high degree were mainly distributed in the frontal lobe and the central, while the nodes with high betweenness centrality were mainly distributed in the parietal lobe, the central and top occipital area. This study helps to reveal the influence of acupoint magnetic stimulation on brain functional networks.