Plant adapted in the fragile zone offer enormous opportunity to understand the stress biology under ecological scenario . Stipa capillacea is widely distributed in the frigid and arid region of Tibet Plateau, but its signal system has never been investigated yet. In this study, we isolated a signal transduction gene, ScCBL6 , in Stipa capillacea , to characterize its cold tolerance capacity by ectopic expression in Arabidopsis . The results suggested that full length ScCBL6 encodes 227 amino acids, and phylogenetically clustered with CBL6 protein in Stipa purpurea and Oryza sativa . In comparison with wild type (WT) plants, ScCBL6 overexpressing plants ( ScCBL6- OXP) are tolerant to cold stress but not drought stress, which attested by the higher photosynthetic capacity (Fv/Fm) and survival rate of ScCBL6- OXP under cold stress. We further compared their cold-responsive transcriptome profiles through RNA-Seq. Totally, 3931 genes were differentially expressed by introduction of ScCBL6. They are participated in multiple processes like immune system, lipid catabolic, secondary metabolic and mainly enriched in plant hormone signal transduction and biomacro-molecule metabolism as regard to KEGG pathway. Differential expressed genes (DEGs) were predicted to locate in chloroplast, mitochondrion, vacuole, and so on, suggesting multitudinous function of ScCBL6. Based on the integrated analysis of ScCBL6-OXP, we inferred that ScCBL6 improve plant cold stress tolerance via regulate photosynthesis redox and vacuole metabolites transport in Arabidopsis .