Social anxiety is characterized by an intense fear of evaluation from others and/or withdrawal from social situations. Extreme social anxiety can lead to social anxiety disorder. There remains an urgent need to investigate the neural substrates of subclinical social anxiety for early diagnosis and intervention to reduce the risk to develop social anxiety disorder. Twenty-nine young adults were recruited (10 males/19 females; mean age (SD) = 20.34 (2.29)). Trait-like social anxiety was assessed by Liebowitz Social Anxiety Scale. Functional magnetic resonance imaging was used with an emotional face-matching paradigm to probe brain activation in response to emotional stimuli including angry, fearful, and happy faces, with shape-matching as a control condition. Behavioral results showed positive correlations between Liebowitz Social Anxiety Scale scores and the reaction time in both angry and fearful conditions. The activation of superficial amygdala and the deactivation of basal forebrain in response to angry condition showed positive correlations with the level of social anxiety. In addition, the resting-state functional connectivity between these two regions was negatively correlated with the level of social anxiety. These results may help to understand the individual difference and corresponding neural underpinnings of social anxiety in the subclinical population, and might provide some insight to develop strategies for early diagnosis and interventions of social anxiety to reduce the risk of deterioration from subclinical to clinical level of social anxiety.