Introduction Effort-reward imbalance (ERI) is a typical psychosocial stress. Schizotypal traits are attenuated features of schizophrenia in the general population. According to the diathesis-stress model, schizotypal traits and psychosocial stress contribute to the onset of schizophrenia. However, few studies examined the effects of these factors on brain alterations. This study aimed to examine relationships between ERI, schizotypal traits and brain structures and functions. Methods We recruited 37 (13 male, 24 female) participants with high levels of schizotypal traits and 36 (12 male, 24 female) participants with low levels of schizotypal traits by the Schizotypal Personality Questionnaire (SPQ). The Chinese school version of the effort-reward imbalance questionnaire (C-ERI-S) was used to measure ERI. We conducted the voxel-based morphometry (VBM) and whole brain resting-state functional connectivity (rsFC) analysis using reward or stress-related regions as seeds. Results Participants with high levels of schizotypal traits were more likely to perceive ERI. The severity of ERI was correlated with grey matter volume (GMV) reduction of the left pallidum and altered rsFC among the prefrontal, striatum and cerebellum in participants with high levels of schizotypal traits. Conclusion ERI is associated with GMV reduction and altered rsFC in individuals with high levels of schizotypal traits.