Paired associated stimulation (PAS) has been confirmed to play a role in motor recovery after stroke, but the underlying mechanism has not been fully elucidated. In this study, we employed a comprehensive battery of measurements, including behavioral test, electrophysiology and H-1-NMR approaches, to investigate the therapeutic effects of PAS in rat model of cerebral ischemia and its underlying mechanism. Rats were randomly divided into a transient middle cerebral artery occlusion group (tMCAO group), a tMCAO + PAS group (PAS group), and a sham group. PAS was applied over 7 consecutive days in PAS group. The behavioral function of rats was evaluated by modified Garcia Scores and Rota-rod test. Electrophysiological changes were measured by motor evoked potentials (MEP). Metabolic changes of ischemic penumbra were detected by H-1-NMR. After PAS intervention, the performances on Rota-rod test and Garcia test improved and the amplitude of MEP increased significantly. The gamma-aminobutyric acid (GABA) in penumbra cortex was decreased significantly, whereas the glutamate showed the opposite changes. The results suggested that post-stroke recovery promoted by PAS may be related to the metabolites alteration in ischemic penumbra and also regulate the excitability of motor cortex.