As one of the most common cancers，Gastric cancer (GC) exhibits high incidence and mortality. Recent studies have indicated that serum f tumor markers can provide valuable diagnostic information for GC. In this study, we examine the clinicopathological significance of preoperative serum tumor markers and serum metabolites on gastric adenocarcinoma patients. We first perform the serum metabolic profiling of 139 gastric adenocarcinoma patients and 156 healthy controls by the Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Based on these chemometric results, we then identify three metabolites, namely phosphatidylcholine (PC) (34:1), palmitoyl-L-carnitine and m/z 361.234, as “potential marker metabolites”. Finally, we perform the ROC curve analysis on the three potential marker metabolites to distinguish the 12 early gastric adenocarcinoma patients from healthy controls. Our analysis has yielded an AUC of 0.973, with 91.7% on sensitivity and 93.6% on specificity at the best cutoff point. Our study has empirically shown that serum metabolomics is amenable for the minimally invasive diagnosis of human gastric adenocarcinoma.