Abstract: The purpose of this study was to explore the effect of rTMS on the interaction of the cerebral cortex in the brain functional network.Based on graph theory,complex network theory was used to analyze the function of the brain electrical signal evoked by transcranial magnetic stimulation in the cortex.With rTMS on the motor area of the brain,the brain functional network were constructed under the quiet state,the EEG signal of magnetic stimulation motor area under the condition of the parameters on the global network of brain function and local parameters were analyzed statistically and by visual image.It was found that there was a significant change in the global and local parameters of the brain function network under the condition of magnetic stimulation motor area comparing with the condition of quiet,and the difference was statistically significant.