(1) Background: Accurate localization of the epileptogenic zone and understanding the related functional connectivity (FC) alterations are critical for the prediction of clinical prognosis in patients with temporal lobe epilepsy (TLE). We aim to localize the hypometabolic region in TLE patients, compare the differences in FC alterations based on hypometabolic region and structural lesion, respectively, and explore their relationships with clinical prognosis. (2) Methods: Thirty-two TLE patients and 26 controls were recruited. Patients underwent 18F-FDG PET/MR scan, surgical treatment, and a 2-3-year follow-up. Visual assessment and voxel-wise analyses were performed to identify hypometabolic regions. ROI-based FC analyses were performed. Relationships between clinical prognosis and FC values were performed by using Pearson correlation analyses and receiver operating characteristic (ROC) analysis. (3) Results: Hypometabolic regions in TLE patients were found in the ipsilateral hippocampus, parahippocampal gyrus, and temporal lobe (p < 0.001). Functional alterations based on hypometabolic regions showed a more extensive whole-brain FC reduction. FC values of these regions negatively correlated with epilepsy duration (p < 0.05), and the ROC curve of them showed significant accuracy in predicting postsurgical outcome. (4) Conclusions: In TLE patients, FC related with hypometabolic region obtained by PET/fMRI may provide value in the prediction of disease progression and seizure-free outcome.