Objective: To compare the metabolites of in vivo 1H- MRS in pancreatic cancer with normal pancreas, and correlate these metabolites with Positron Emission Tomography (PET) metabolic activity, clinical stages, and survival outcomes. Methods: The prospective study included 58 patients (mean age 62.7 ± 12.1 years, range 34–81 years; 36 men, 22 women) with pathological proof of pancreatic adenocarcinoma, and all of them received 18F-fluorodeoxyglucose (FDG) PET/MRI before treatment. The single-voxel MRS with a point-resolved selective spectroscopy sequence was used to measure metabolites (creatine, Glx (glutamine and glutamate), N-acetylaspartate (NAA), and lipid) of pancreatic cancer and adjacent normal parenchyma, respectively. FDG-PET parameters included SUVmax, metabolic tumor volume (MTV), and total lesion glycolysis (TLG). Non-parametric tests were used to evaluate the differences of MRS metabolites between pancreatic cancer and those in normal pancreas, and their correlation with PET parameters and clinical stages. The correlation with progression-free survival (PFS) and overall survival (OS) was measured using the Kaplan–Meier and Cox proportional hazard models. Results: When compared with normal pancreas, the Glx, NAA, and lipid levels were significantly decreased in pancreatic cancer (all p < 0.05). Creatine, Glx, and lipid levels were all inversely correlated with both MTV (rho = −0.405~−0.454) and TLG (rho = −0.331~−0.441). For correlation with clinical stages, lower lipid levels were found in patients with T4 (vs. <T4, p = 0.038) and lower creatine levels were found in N1 (vs. N0, p = 0.019). Regarding survival outcomes, high TNM stage, low creatine, low Glx, and low lipid levels were associated with both poor PFS and OS (all p < 0.05). Additionally, creatine remained an independent factor for PFS and OS after adjusting for age, sex, tumor size, stages, and other metabolites levels. Conclusions: Decreased MRS metabolites in pancreatic cancer were associated with poor survival outcome, and may be used as prognostic image biomarkers for these patients.