The aim of this study was to explore whether there will be any alterations in sensorimotor-related cortex and the possible causes of sensorimotor dysfunction after incomplete cervical spinal cord injury (ICSCI). Structural and resting-state functional magnetic resonance imaging (rs-fMRI) of nineteen ICSCI patients and nineteen healthy controls (HCs) was acquired. Voxel based morphometry (VBM) and tract-based spatial statistics were performed to assess differences in gray matter volume (GMV) and white matter integrity between ICSCI patients and HCs. Whole brain functional connectivity (FC) was analyzed using the results of VBM as seeds. Associations between the clinical variables and the brain changes were studied. Compared with HCs, ICSCI patients demonstrated reduced GMV in the right fusiform gyrus (FG) and left orbitofrontal cortex (OFC) but no changes in areas directly related to sensorimotor function. There were no significant differences in brain white matter. Additionally, the FC in the left primary sensorimotor cortex and cerebellum decreased when the FG and OFC, respectively, were used as seeds. Subsequent relevance analysis suggests a weak positive correlation between the left OFC’s GMV and visual analog scale (VAS) scores. In conclusion, brain structural changes following ICSCI occur mainly in certain higher cognitive regions, such as the FG and OFC, rather than in the brain areas directly related to sensation or motor control. The functional areas of the brain that are related to cognitive processing may play an important role in sensorimotor dysfunction through the decreased FC with sensorimotor areas after ICSCI. Therefore, cognition-related functional training may play an important role in rehabilitation of sensorimotor function after ICSCI. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.