Early diagnosis is key to improving the prognosis of gastric cancer. Altered phospholipid metabolism has been observed in different types of cancer. This study assessed serum phospholipid levels of patients with gastric cancer to explore biomarkers for its early diagnosis. A total of 199 participants were enrolled, including patients with early gastric cancer or precancerous gastric lesions and healthy controls. Serum phospholipids were extracted and identified using mass spectrometry. The relative abundances of these phospholipids were compared among patients at different disease stages. Twenty-four patients with early gastric cancer were followed up, and their serum phospholipid levels were compared beween before and after resection. Fifty-four phospholipids were identified. Phosphatidylethanolamine (36:3), phosphatidylethanolamine (36:2), phosphatidylcholine (32:0), and sphingomyelin (d18:0/18:1(9Z)) were more abundant in patients with early gastric cancer than in healthy controls. The area under the receiver operating curve of sphingomyelin (d18:0/18:1(9Z)) reached 0.883 in the training set (sensitivity 81.08%, specificity 78.82%) and 0.874 in the validation set. The levels of phosphatidylethanolamine (36:2), phosphatidylcholine (32:0), and sphingomyelin (d18:0/18:1(9Z)) significantly declined after the cancerous lesions were resected. Serum phospholipids can serve as potential biomarkers for the early diagnosis of gastric cancer.