BACKGROUND: Social intelligence refers to an important psychosocial skill set encompassing an array of abilities, including effective self-expression, understanding of social contexts, and acting wisely in social interactions. While there is ample evidence of its importance in various mental health outcomes, particularly social anxiety, little is known on the brain correlates underlying social intelligence and how it can mitigate social anxiety. OBJECTIVE: This research aims to investigate the functional neural markers of social intelligence and their relations to social anxiety. METHODS: Data of resting-state functional magnetic resonance imaging and behavioral measures were collected from 231 normal students aged 16 to 20 years (48% male). Whole-brain voxel-wise correlation analysis was conducted to detect the functional brain clusters related to social intelligence. Correlation and mediation analyses explored the potential role of social intelligence in the linkage of resting-state brain activities to social anxiety. RESULTS: Social intelligence was correlated with neural activities (assessed as the fractional amplitude of low-frequency fluctuations, fALFF) among two key brain clusters in the social cognition networks: negatively correlated in left superior frontal gyrus (SFG) and positively correlated in right middle temporal gyrus. Further, the left SFG fALFF was positively correlated with social anxiety; brain-personality-symptom analysis revealed that this relationship was mediated by social intelligence. CONCLUSION: These results indicate that resting-state activities in the social cognition networks might influence a person's social anxiety via social intelligence: lower left SFG activity → higher social intelligence → lower social anxiety. These may have implication for developing neurobehavioral interventions to mitigate social anxiety.