This study aims to investigate the brain gray matter volume (GMV) alterations of pediatric complete thoracolumbar spinal cord injury without fracture or dislocation (SCIWOFD) using voxel-based morphometry (VBM) analysis and assess the sensitive neuroimaging biomarkers which may be surrogate targets to enhance brain plasticity. A total of 52 pediatric subjects (age range, 6-12 years), including 25 pediatric SCIWOFD patients and 27 typically developing (TD) children were recruited. Independent two-sample t test was performed to assess between-group differences of brain GMV. Partial correlation analyses were performed to explore the correlations between GMV values and ISNCSCI scores, age at the time of injury, time after initial SCI. Receiver operating characteristic (ROC) analysis was performed to compute the sensitivity and specificity of the imaging biomarkers for pediatric SCIWOFD diagnosis. As the results, pediatric SCIWOFD patients showed significantly decreased GMV of bilateral Cerebellum lobule VIII, right middle occipital gyrus (MOG) and putamen (PUT), left pallidum (PAL) and thalamus (THA), and increased GMV of Vermis_III, right Cerebellum lobule VI and SupraMarginal gyrus (SMG). Additionally, GMV of left PAL and right PUT were negatively correlated with the pinprick/light touch sensory scores in pediatric SCIWOFD patients. Finally, when using the GMV values of left PAL and right PUT in combination as the predictor, area under the curve (AUC) reached the highest, of 0.93. These findings provided evidence that the brain undergoes GMV changes following pediatric SCIWOFD, which may suggest important targets for functional remodeling after SCI in children and provide valuable information for the development of novel and effective rehabilitation therapies in the future.