This work aims to explore the roles and mechanisms of long non coding RNA (lncRNA) THOR in regulating the stemness of gastric cancer cells. RNA-sequencing combined with quantitative real-time PCR (qRT-PCR) indicated that lncRNA THOR level was significantly upregulated in gastric cancer tissues compared with that in normal adjacent tissues. Knockdown of THOR attenuated the stemnness of gastric cancer cells, evident by the decrease of stemness markers expression and capacity of cells spheroid formation. Further RNA-sequencing combined with qRT-PCR and western blot analysis demonstrated that expression of transcriptional factor SOX9 was remarkably decreased in gastric cancer cells with THOR stable knockdown. Additionally, RNA immunoprecipitation (RIP) combined with luciferase reporter assay revealed that THOR directly bound to SOX9 3' untranslated region (3'UTR), but not its 5'UTR or coding area. Notably, overexpression of SOX9 rescued THOR knockdown-mediated inhibition on the stemness of gastric cancer cells. Thus, our results suggest that THOR could potentiate the stemness of gastric cancer cells via directly binding to SOX9 3'UTR.