Abstract: Magnetic stimulation has the significant advantages of effective,painless,non-invasive,easy to duplicate and simple operationin the application of central nerve function test and nerve function recovery.Acupoint is the breakthrough point between body surface stimulation and internal nervous system regulation,which is significant in the study of regulatory mechanism of t he brain complex dynamic system and rehabilitation treatment of some diseases.In this paper, Granger causality was used for brain functional network building based on EEG signal under magnetic stimulation at PC6 acupoint,explored the change rule of the causation of the brain during the stimulation.In addition,the features of complex network were comparatively analyzed between the quiescent and stimulated states.Our experimental results show the information flow of the brain system at the quiescent state is balanced.The power of the GC was increased,the flow of information was mainly from the frontal lobe to the occipital lobe,the central intensity of C4 in parietal lobe was significantly increased,the efficiency of information transmission was improved and the "small-world" property was stronger through stimulating PC6 acupoint.