The aim of this study is to explore the effects of continuous theta-burst transcranial magnetic stimulation (cTBS) on functional brain network in emotion processing. Before and after the intervention of cTBS over left dorsolateral prefrontal cortex (DLPFC) of ten participants who were asked to perform the emotion gender recognition task, we recorded their scalp electroencephalograms (EEG). Then we used the phase synchronization of EEG to measure the connectivity between two nodes. We then calculated the network efficiency to describe the efficiency of information transmission in brain regions. Our research showed that after the intervention of cTBS and the stimulation of the emotion face picture, there was an obvious enhancement in the event-related spectral perturbation after stimuli onset in beta band in 100–300 ms. Under the stimulation of different emotion picture, the values of global phase synchronization for negative and neutral stimuli were enhanced compared to positive ones. And the increased small-worldness was found in emotional processing. In summary, based on the effect of activity change in the left DLPFC on emotion processing brain network, the emotional processing mechanism of brain networks were preliminary explored and it provided the reference for the research of emotion processing brain network in the future.