Individuals with autism-like traits (ALT) belong to a subclinical group with similar social deficits as autism spectrum disorders (ASD). Their main social deficits include atypical eye contact and difficulty in understanding facial expressions, both of which are associated with an abnormality of the right posterior superior temporal sulcus (rpSTS). It is still undetermined whether it is possible to improve the social function of ALT individuals through noninvasive neural modulation. To this end, we randomly assigned ALT individuals into the real (n=16) and sham (n=16) stimulation groups. All subjects received five consecutive days of intermittent theta burst stimulation (iTBS) on the rpSTS. Eye tracking data and functional magnetic resonance imaging (fMRI) data were acquired on the first and sixth days. The real group showed significant improvement in emotion recognition accuracy after iTBS, but the change was not significantly larger than that in the sham group. Resting-state functional connectivity (rsFC) between the rpSTS and the left cerebellum significantly decreased in the real group than the sham group after iTBS. At baseline, rsFC in the left cerebellum was negatively correlated with emotion recognition accuracy. Our findings indicated that iTBS of the rpSTS could improve emotion perception of ALT individuals by modulating associated neural networks. This stimulation protocol could be a vital therapeutic strategy for the treatment of ASD.