Accumulated knowledge indicates that phantom limb pain is a phenomenon of the central nervous system that is related to plastic changes at several levels of the nervous systems. Especially, reports using patients with neuropathic pain clearly indicate the sensorimotor cortex as underlying mechanisms of phantom limb and its pain. Here, we focus the notion that limb amputation or deafferentation results in plasticity of connections between the brain and the body, and that the cortical motor representation of the missing or deafferented limb seemingly disappears. Meanwhile, the sensory representation of the limb does not disappear and thereby patients feel phantom limbs. We propose that dissociation between motor and sensory representations in the primary motor cortex induces pathologic pain and reconcile of sensorimotor integration of the limb would alleviate pain, on the basis of our neurorehabilitation approaches and artificial neuromodulation strategies.