Background: Motor dysfunction is the main functional disability after spinal cord injury (SCI), seriously affecting the life and work of patients. In addition to spinal cord damage, the brain undergoes structural and functional plastic changes. This study explored brain function remodeling in patients with SCI and the effect of right ankle dorsiflexion motor imagery task on brain function. Methods: This prospective study enrolled 11 patients with SCI and dyskinesia of the right lower limb and 12 healthy subjects at the General Hospital of Western Theater Command PLA (January 2015 to December 2016). They underwent functional magnetic resonance imaging (fMRI) in the resting state and the “right ankle dorsiflexion” motor imagery task state. Four-dimensional (spatiotemporal) concordance (FOCA) of local neuronal activity was used for fMRI image analysis. The differences between SCI patients and healthy subjects were compared using the two-sample t-test. Results: In the resting state, compared with healthy subjects, patients with SCI showed decreased FOCA in the left putamen, right caudate nucleus, and right superior occipital gyrus and increased FOCA in the left precentral gyrus. In the right ankle dorsiflexion motor imagery task state, FOCAs in the right inferior temporal gyrus and left inferior parietal lobule were decreased in patients with SCI. Conclusions: After SCI, a series of changes in the structure and function of the brain occur. Research on brain plasticity after SCI might help explore the central mechanisms underlying functional recovery after treatments, providing more therapeutic strategies for SCI.