In this study, we observed pediatric complete spinal cord injury (CSCI) patients receiving MI training and divided them into different groups according to the effect of motor imagery (MI) training on neuropathic pain (NP). Then, we retrospectively analysed the differences in brain structure of these groups before the MI training, identifying brain regions that may predict the effect of MI on NP. Thirty pediatric CSCI patients were included, including 12 patients who experienced NP during MI and 18 patients who did not experience NP during MI according to the MI training follow-up. The 3D high-resolution T1-weighted images of all subjects were obtained using a 3.0 T MRI system before MI training. A two-sample t-test was performed to evaluate the differences in gray matter volume (GMV) between patients who experienced NP and those who did not experience NP during MI. Receiver operating characteristic (ROC) analysis was performed to compute the sensitivity and specificity of the imaging biomarkers for the effect of MI on NP in pediatric CSCI patients. MI evoked NP in some of the pediatric CSCI patients. Compared with patients who did not experience NP, patients who experienced NP during MI showed larger GMV in the right primary sensorimotor cortex (PSMC) and insula. When using the GMV of the right PSMC and insula in combination as a predictor, the area under the curve (AUC) reached 0.824. Our study demonstrated that MI could evoke NP in some pediatric CSCI patients, but not in others. The individual differences in brain reorganization of the right PSMC and insula may contribute to the different effects of MI on NP. Moreover, the GMV of the right PSMC and insula in combination may be an effective indicator for screening pediatric CSCI patients before MI training therapy.© 2024 The Authors. Published by Elsevier Ltd.