Background: Impairment in facial emotion perception is an important domain of social cognition deficits in schizophrenia. Although impaired facial emotion perception has been found in individuals with negative schizotypy (NS), little is known about the corresponding change in brain functional connectivity. Methods: Sixty-four participants were classified into a high NS group (n = 34) and a low NS group (n = 30) based on their total scores on the Chapman scales for physical and social anhedonia. All participants undertook a facial emotion discrimination functional imaging task that consisted of four emotional valences (angry, fear, happy, and neutral). For univariate analysis, the signal change at the bilateral amygdala was compared for each emotional contrast using SPSS (P < .05). For the functional connectivity analysis, we calculated the beta-series functional connectivity of the bilateral amygdala with the medial prefrontal cortex (mPFC) and compared the group differences in SPM12 (P < .05, small volume family-wise error correction). Results: No significant differences were found between the high and low NS groups in accuracy and reaction time in the facial emotion discrimination task. The high NS group showed reduced brain activations at the amygdala under fearful and neutral conditions. Reduced functional connectivity between the amygdala and the mPFC/dorsal anterior cingulate cortex under the happy and fearful conditions in the high NS group was also found. Conclusions: Our findings suggest that the individuals with high NS showed altered brain activity and functional connectivity at the amygdala during facial emotion processing and provide new evidence for understanding social cognition deficits in at-risk individuals.