Brain gray matter (GM) and white matter alterations have been studied in pediatric spinal cord injury (SCI) patients. However, the differences in brain reorganization between complete SCI (CSCI) and incomplete SCI (ICSCI) remain unclear. The objective of the study was to explore the different effects of CSCI and ICSCI on brain structure in pediatric patients. A total of 68 children with SCI (37 with CSCI and 31 with ICSCI) and 36 age-matched healthy controls (HCs) were enrolled. The clinical data on motor and sensory scores, degree of injury, duration of injury, and age at the time of injury were assessed. GM volume (GMV) and diffusion tensor imaging (DTI) indices were analyzed using voxel-based morphometry and tract-based spatial statistics. Both CSCI and ICSCI patients exhibited abnormalities in GMV and DTI metrics within brain regions associated with sensorimotor functions, emotional processing, and pain perception. Notably, the ICSCI group showed significantly reduced GMV in the left thalamus (p < 0.001, t = - 5.275), right caudate nucleus (p < 0.001, t = - 4.992), and left precuneus (p = 0.002, t = - 4.053) compared to the CSCI group. Our study showed that pediatric patients with CSCI and ICSCI exhibit distinct patterns of GM reorganization in regions involved in sensory processing and cognitive functions.© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.