In this study we investigated the role right prefrontal cortex played on emotion-related processing while applying the active intervention by continuous theta burst stimulation (TBS). Electroencephalography (EEG) activities were recorded in 14 healthy subjects when they performed an emotional recognition task for facial expressions. TBS was delivered over dorsolateral prefrontal cortex (DLPFC) between a set of tasks. In order to time-variant characteristic in the dynamic brain, event-related spectral perturbation (ERSP) was calculated within alpha frequency bands (8–13Hz) for four time windows (1–200ms, 201–400ms, 401–600ms and 601–800ms). We found that the react time of positive stimuli is lower than negative stimuli, but no difference for both emotions was observed between pre-TBS and post-TBS nor for accuracy; the significant decreased of ERSP after TBS were found in alpha band in left prefrontal cortex, indicating the obvious activation. Our results support mechanism of interhemispheric competition, and also demonstrate the important role of right prefrontal cortex in processing emotion-related attention.