Objective To investigate the overall serum metabolic differences between pancreatic cancer and healthy controls and screen the different metabolites as potential diagnostic marker for early diagnosis of pancreatic cancer. Methods Case control group analysis method was used,and patients with pathological diagnosis of pancreatic ductal adenocarcinoma were considered as case group, and healthy subjects were considered as control group. UHPLC/Q-TOF MS-based metabonomics techniques were applied to analyze the difference in serum metabolites in the two groups with multivariate and univariate statistical method, and the different metabolites were screened and identified in accordance with the molecular weight, metabolites databases and MS/MS information. The diagnostic discrimination of the different metabolites was evaluated by ROC curve. Results In this study, there were 54 patients with pathological diagnosis of pancreatic ductal adenocarcinoma and 54 age and sex matched healthy controls. There were 12 kinds of different serum metabolits in the final screening and identification in the two groups. The level of hydroxy-arachidonic acid, phenylalanine, acetylcarnitine, linoleic acid, palmitoylcarnitine, linoleyl carnitine, and uracil deoxynucleotide and glycocholic chenodeoxycholic acid in serum of pancreatic cancer patients were higher than those in the controls (P ＜ 0.05). Serum LysoPC (18∶ 0), LysoPC (P-16∶ 0), LPA (18:2 / 0:0), LysoPC (14:0) in patients with pancreatic ductal adenocarcinoma were lower than those in the controls (P < 0.05). The AUC of HETE, LysoPC (18:0), phenylalanine, LPA (18:2 / 0:0), dUMP was 0.98, 0.96, 0.92, 0.91, respectively, which were significantly higher than that of CA19-9 (0.90). Conclusions Twelve kinds of different serum metabolits are screened and identified between pancreatic ductal adenocarcinoma patients and healthy subjects, and HETE, LysoPC (18:0), phenylalanine, LPA(18:2 / 0:0), dUMP may be potential markers for diagnosis of pancreatic cancer.