Objective: Investigating structural changes in the cervical spinal cord and brain in children with complete thoracolumbar spinal cord injury (TLSCI) and their correlation with clinical function may provide objective imaging indicators for functional evaluation.Methods: Twenty-one children with complete TLSCI and twenty-one typically developing (TD) children were enrolled in this study. All participants underwent whole-brain and upper cervical spinal cord sagittal 3D T1-weighted and whole-brain axial diffusion tensor imaging scans using a 3.0T MRI scanner. Utilizing the Spinal Cord Toolbox, cervical spinal cord morphological parameters were obtained. Brain structure changes were analyzed with voxel-based morphometry (VBM) and voxel-based analysis (VBA).Results: Compared to TD children, children with TLSCI showed significant reductions in the CSA (P = .011) and APW (P = .002) at the C2/3 level, as well as significant atrophy in the gray matter volume (GMV) of the left thalamus (P = .026), and bilateral paracentral lobule (PCL, P = .002). There was a significant positive correlation (r = 0.540, P = .017) between GMV of bilateral PCL and sensory scores. The VBA results showed a significant increase in fractional anisotropy values in the right posterior limb of the internal capsule, posterior thalamic radiation, and superior longitudinal fasciculus (SLF, P = .045), the mean diffusivity value of the right SLF was significantly decreased (P = .049) in children with TLSCI.Conclusions: In children with complete TLSCI, specific structural changes in the cervical spinal cord and brain were observed. A significant correlation between GMV of bilateral PCL and sensory scores may provide imaging biomarkers for assessing neurologic function and therapeutic efficacy (Ethics No: [2020] 003).