Abstract: It is still controversial whether acupoint specificity exists.The different effects of magnetic stimulation of Hegu and Waiguan were investigated from the perspective of complex networks for the first time.Electroencephalogram data of two groups during resting state and magnetic stimulation were collected and preprocessed.Correlation coefficients between any two channels were calculated and then were analyzed statistically.Node strengths and betweenness centrality were computed.Results showed that magnetic stimulation of Waiguan had a significant effect on connections not only between the left frontal and parietal, occipital lobes, but also the connections between right frontal and left occipital, compared to Hegu.Node strengths and betweenness centrality have significantly different changes over brain regions.The study confirmed again that magnetic stimulation of acupoint can change the cortical plasticity and also provide a theoretical basis for acupoint specificity to some degree.