AbstractOwing to the limitations of cross‐sectional studies, it is unclear whether social media induce brain changes, or if individuals with certain biological traits are more likely to use social media. Functional connectivity (FC) can reflect cerebral functional plasticity, and if social media can influence cerebral FC, then the FC of light social media users should be more similar to that of heavy users after they “heavily” used social media for a long period. We combined longitudinal study design and intersubject correlation (ISC) analysis to investigate this similarity. Thirty‐five heavy and 21 light social media users underwent cognitive tests and functional MRIs. The 21 light social media users underwent another functional MRI scan after completing an additional four‐week social media task. We conducted the ISC at the group, individual, and brain‐region levels to investigate the similarity of FC and locate the brain regions most affected by social media. The FC of light social media users was more similar to that of heavy social media users after they completed the four‐week social media task. Then, social media had an impact on half of the brain, involving almost all brain networks. Finally, cerebral FC that mostly affected by social media was associated with selective attention. We concluded that the impact of social media use on cerebral functional connectivity changes is revealed by ISC method and longitudinal design, which may provide guidance for clinical practice. The methods used in the current research could also be applied to similar domains.