Motor imagery (MI) engages a broad network of brain regions to imagine a specific action. Investigating the mechanism of brain network reorganization during MI after spinal cord injury (SCI) is crucial because it reflects overall brain activity. Using electroencephalogram (EEG) data from SCI patients, we conducted EEG-based coherence analysis to examine different brain network reorganizations across different frequency bands, from resting to MI. Furthermore, we introduced a consistency calculation-based residual graph convolution (C-ResGCN) classification algorithm. The results show that the [Formula: see text]- and [Formula: see text]-band connectivity weakens, and brain activity decreases during the MI task compared to the resting state. In contrast, the [Formula: see text]-band connectivity increases in motor regions while the default mode network activity declines during MI. Our C-ResGCN algorithm showed excellent performance, achieving a maximum classification accuracy of 96.25%, highlighting its reliability and stability. These findings suggest that brain reorganization in SCI patients reallocates relevant brain resources from the resting state to MI, and effective network reorganization correlates with improved MI performance. This study offers new insights into the mechanisms of MI and potential biomarkers for evaluating rehabilitation outcomes in patients with SCI.