This study aimed to investigate whether brain anatomical structures and functional network connectivity are altered after chronic complete thoracic spinal cord injury (cctSCI) and to determine how these changes impact clinical outcomes. Structural and resting-state functional MRI was performed for 19 cctSCI patients (18 for final statistics) and 19 healthy controls. Voxel-based morphometry (VBM) was used to assess gray matter volume (GMV) with differences between cctSCI patients and controls. VBM results were used as seeds for whole-brain functional connectivity (FC) analysis. The relationship between brain changes and clinical variables was investigated. Compared with those of the control group, the left triangular inferior frontal gyrus, middle frontal gyrus, orbital inferior frontal gyrus, precuneus and parietal superior gyrus volumes of SCI patients decreased, while the left superior frontal gyrus and supplementary motor area volumes increased. Additionally, when the regions with increased GMV were used as seeds, the FC of the parahippocampus and thalamus increased. Subsequent partial correlation analysis showed a positive correlation between FC and total sensorimotor score based on the ASIA criteria (p = 0.001, r = 0.746). Overall, the structural and functional changes in the brain after cctSCI occurred in some visual and cognitive areas and sensory or motor control areas. These findings aid in improving our understanding of the underlying brain injury mechanisms and the subsequent structural and functional reorganization to reveal potential therapeutic targets and track treatment outcomes.Copyright © 2023. Published by Elsevier B.V.