To cure the impaired physiological functions after the spinal cord injury, not only development of molecular therapies for axonal regeneration, but also that of therapeutic strategies to induce appropriate rewiring of neural circuits should be necessary. For this purpose, understanding the plastic changes in the central nervous system during spontaneous recovery following the injury would be helpful. In this article, a series of studies conducted in the authors’ laboratory on the reorganization of neural networks in the partial spinal cord injury model using macaque monkeys are reviewed. In this model, after selective lesion of the lateral corticospinal tract at the fifth cervical segment, dexterous digit movements are once impaired, but recover through rehabilitative training in a few weeks to a few months. During the recovery, synaptic transmission and organization of the neural circuits exhibit drastic changes depending on the time after the injury, not only in the spinal cord, but also in hierarchically higher order structures such as motor-related cortical areas and even in limbic structures. It is suggested that on top of the molecular therapies, neurorehabilitative and neuromodulatory therapies targeting such higher order structures should be helpful in inducing appropriate rewiring of the neural circuits.