Purpose Differentiating mesial temporal lobe epilepsy (MTLE) and neocortical temporal lobe epilepsy (NTLE) remains a challenge. Our study aimed at characterization of the metabolic profiles between MTLE and NTLE, as well as their correlation with surgical prognosis by using 18F-FDG-PET. Methods In total, 137 patients with intractable TLE and 40 age-matched healthy controls were recruited. Patients were divided into MTLE group (N = 91) and NTLE group (N = 46). 18F-FDG-PET was used to measure the metabolism of regional cerebra, which was analyzed by statistical parametric mapping. The volume of abnormal metabolism in cerebral regions and their relationship with surgical prognosis were calculated for each surgical patient. Results The cerebral hypometabolism of MTLE is limited to the ipsilateral temporal and insular lobes (p<0.001, uncorrected), while the NTLE patients showed hypometabolism in the ipsilateral temporal, frontal and parietal lobes (p<0.001, uncorrected). The MTLE patients showed extensive hypermetabolism in cerebral regions (p<0.001, uncorrected). Hypermetabolism in NTLE is limited to contralateral temporal lobe and cerebellum, ipsilateral frontal, occipital lobe, and bilateral thalamus (p<0.001, uncorrected). Among patients who underwent resection of epileptic lesions, 51 (67.1%) patients in the MTLE group and 10 (43.5%) in NTLE achieved an Engel class IA outcome (p=0.041). In the MTLE group, the volumes of metabolic increase for frontal lobe or thalamus were larger in non-Engel class IA patients than in Engel class IA patients (p<0.05). Conclusion Spatial metabolic profile could discriminate NTLE from MTLE. In MTLE, hypermetabolism of thalamus and frontal lobe could facilitate preoperative counseling and surgical planning.