To study the brain functional alterations of children after spinal cord injury (SCI) and explore their changes after motor imagery training (MIT), revealing brain functional reorganizations in pediatric SCI and finding possible neural mechanisms of MIT. Thirty pediatric SCI patients and 30 age- and gender-matched healthy controls (HCs) were recruited. Brain resting-state functional MRI images of all subjects were obtained using a 3.0 Tesla MRI system. Subsequently, eight of the patients completed a 4-week MIT, and then functional MRI scans were conducted once again. Then two-sample t-tests were used to compare amplitude of low frequency (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo) between groups at baseline, and paired t-tests were used to investigate the changes in ALFF, fALFF and ReHo of patients before and after the treatment. Compared with HCs, the patients showed decreased ALFF and/or ReHo in bilateral postcentral gyrus (S1) and right orbitofrontal cortex, while increased ALFF and/or ReHo in the bilateral cerebellar lobules IV-VI, thalamus, left middle cingulate cortex (MCC), cerebellar Crus II, and right parahippocampal gyrus, caudate nucleus, middle temporal gyrus (MTG). Compared with those before MIT, the patients showed significantly increased ALFF in the right S1 after the treatment. These findings demonstrated brain functional reorganization in sensoriomotor, cognitive-emotional and auditory/language related regions, and MIT may promote the rehabilitation by reversing the functionally reorganized sensoriomotor areas, which may provide a possible mechanism for MIT.© 2025 Published by Elsevier Inc. on behalf of International Brain Research Organization.