Impaired capability for understanding and interpreting the expressions on other people's faces manifests itself as a core feature of schizophrenia, contributing to social dysfunction. With the purpose of better understanding of the neurobiological basis of facial emotion perception deficits in schizophrenia, we investigated facial emotion perception abilities and regional structural brain abnormalities in drug-naïve patients with first-episode schizophrenia, and then examined the correlation between them. Fifty-two drug-naive patients with first-episode schizophrenia and 29 group-matched healthy controls were examined for facial emotion perception abilities assessed with the Facial Emotion Categorization and performed magnetic resonance imaging. The Facial Emotion Categorization data were inserted into a logistic function model so as to calculate shift point and slope as outcome measurements. Voxel-based morphometry was applied to investigate regional grey matter volume (GMV) alterations. The relationship between facial emotion perception and GMV was explored in patients using voxel-wise correlation analysis within brain regions that showed a significant GMV alterations in patients compared with controls. The schizophrenic patients performed differently on Facial Emotion Categorization tasks from the controls and presented a higher shift point and a steeper slope. Relative to the controls, patients showed GMV reductions in the superior temporal gyrus, middle occipital gyrus, parahippocampa gyrus, posterior cingulate, the culmen of cerebellum anterior lobe, cerebellar tonsil, and the declive of cerebellum posterior lobe. Importantly, abnormal performance on Facial Emotion Categorization was found correlated with GMV alterations in the culmen of cerebellum anterior lobe in schizophrenia. This study suggests that reduced GMV in the culmen of cerebellum anterior lobe occurs in first-episode schizophrenia, constituting a potential neuropathological basis for the impaired facial emotion perception in schizophrenia.