Central neurologic injury (CNI) causes dysfunctions not only in limbs but also in cognitive ability. We applied a novel peripheral nerve rewiring (PNR) surgical procedure to restore limb function. Here, we conducted a prospective study to develop estimates for the extent of preattentive processes to cognitive function changes in CNI patients after PNR. Auditory mismatch negativity (MMN) was measured in CNI patients who received the PNR surgery plus conventional rehabilitation treatment. During the 2-year follow-up, the MMN was enhanced with increased amplitude in the PNR plus rehabilitation group compared to the rehabilitation-only group as the experiment progressed, and progressive improvement in behavioural examination tests was also observed. Furthermore, we found a significant correlation between the changes in Fugl-Meyer assessment scale scores and in MMN amplitudes. These results suggested that PNR could affect the efficiency of pre-attention information processing synchronously with the recovery of motor function in the paralyzed arm of the in chronic CNI patients. Such electroencephalographic measures might provide a biological approach with which to distinguish patient subgroups after surgery, and the change in MMN may serve as an objective auxiliary index, indicating the degree of motor recovery and brain cognitive function.