With high-throughput omics techniques, the gastric cancer-related molecular markers were screened, and the biological functions of candidate gastric cancer molecular markers were studied. The results indicated that IPO-38, gastrin, IL-33, and FAM5C and MYLK methylation in circulation might serve as markers for early diagnosis of gastric cancer. It was also revealed that FRZB, TXNL2, PHF10, MPS-1 and PTP1B were highly expressed in tissues of gastric cancer, which was associated with the proliferation, differentiation, apoptosis and invasion of tumor cells. The high expression of AE1 in gastric cells might keep p16 in cytoplasm, and refrain it from entering nuclei, which served as proto-oncogene. IRX1 and miR-126 were weakly expressed in tissues of gastric cancer, which served as anti-oncogene. The research lays a good foundation for the clinical translational research of screening of candidate gastric cancer markers, development of diagnostics, molecular targets for therapeutics and prognosis prediction. The research findings have won the second prize of National Science Progress in 2008 and first prize of Shanghai Science Progress in 2012.