Linc00641 plays different roles in various types of human cancers. However, the function of linc00641 and its underlying mechanism of action in gastric cancer have not been fully elucidated. Therefore, the aim of our current study was to explore the molecular mechanism of linc00641 in gastric cancer. MTT assays, flow cytometry, wound healing assays, and Transwell invasion assays were utilized to measure cell viability, apoptosis, migration and invasion, respectively. Western blotting and RT-PCR assays were carried out to explore the mechanism of linc00641 in gastric cancer cells. We found that silencing linc00641 suppressed the viability and stimulated the apoptosis of gastric cancer cells, while linc00641 overexpression had the opposite effects. Moreover, linc00641 sponged the expression of miR-429 and subsequently upregulated Notch-1 expression in gastric cancer cells. We concluded that linc00641 promoted the malignant progression of gastric cancer by modulating the miR-429/Notch-1 axis.