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Objective This study used functional magnetic resonance imaging (fMRI) to explore brain structural and related network changes in patients with spinal cord injury (SCI). Methods Thirty-one right-handed SCI patients and 31 gender- and age-matched healthy controls (HC) were included. The gray matter volume (GMV) changes in SCI patients were observed using voxel-based morphometry (VBM). Then, these altered gray matter clusters were used as the regions of interest (ROIs) for whole-brain functional connectivity (FC) analysis to detect related functional changes. The potential association between GMV and FC values with the visual analog scale (VAS), the American Spinal Injury Association (ASIA) score, and the course of injuries was investigated through partial correlation analysis. Results GMV of the frontal, temporal, and insular cortices was lower in the SCI group than in the HC group. No GMV changes were found in the primary sensorimotor area in the SCI group. Besides, the altered FC regions were not in the primary sensorimotor area but in the cingulate gyrus, supplementary motor area, precuneus, frontal lobe, and insular. Additionally, some of these altered GMV and FC regions were correlated with ASIA motor scores, indicating that higher cognitive regions can affect motor function in SCI patients. Conclusions This study demonstrated that gray matter and related network reorganization in patients with SCI occurred in higher cognitive regions. Future rehabilitation strategies should focus more on cognitive functions.