To study the metabolic changes following amputation, we investigated the metabolite concentrations in the secondary somatosensory cortex and thalamus from twenty-three upper limb amputees and sixteen age-matched healthy controls using proton magnetic resonance spectroscopy (MRS). The ratios of major metabolites to the creatine (Cr) peak were quantified to indicate metabolite levels. Compared with the healthy controls, the amputees showed significantly reduced NAA/Cr and Cho/Cr ratios in the secondary somatosensory cortex and thalamus contralateral to the amputation side, indicating neuronal loss and dysfunctions in these brain regions due to the loss of sensory input. Meanwhile, the stump sensation was found to be positively correlated with NAA/Cr ratio and negatively correlated with GSH/Cr ratio in the thalamus. The results suggested that both the thalamus and somatosensory cortex may undergo metabolic changes after amputation.