The prolonged survival of traumatic spinal cord injury (TSCI) patients underscores the need to customize rehabilitative treatment plans according to patients' characteristics, aiming to restore motor function. We conducted a cross-sectional study of two groups with chronic TSCI (short-term group: 11 patients with an injury time of 1-2 years; long-term group: 10 patients with an injury time > 2 years) and 16 controls. Quantitative MRI was used to evaluate structural changes in the upper spinal cord and brain. Compared to controls, both groups exhibited decreased fractional anisotropy (close relationship of the decreased) in the spinal cord, and the long-term group showed reduced spinal cord cross-sectional areas. The short-term group presented increased gray matter volumes (GMVs) in the paracentral lobule, postcentral gyrus, and supplementary motor area, indicating compensatory neural changes, whereas the long-term group exhibited decreased GMV in cerebellar lobule VI, suggesting weakening of the signal received by the cerebellum. Track-based spatial statistics revealed the close relationship of the decreased FA was with the increased radial diffusivity in the long-term group, indicating that demyelination mainly altered the white matter. Correlation analysis revealed that the increased GMV was negatively correlated with the sensorimotor score (r = -0.725, p = 0.018). Additionally, the GMV of cerebellar lobule VI was positively correlated with the sensorimotor score (r = 0.671, p = 0.024). In summary, quantitative MRI identifies structural changes in the brain and spinal cord of patients with chronic TSCI that vary with the time since injury and provide imaging evidence for the development of precise targeted therapies.