Saussurea inversa Raab-Straube is a typical alpine plant, having developed aerenchyma is the most representative structural feature. This study cloned the aerenchyma related gene (ShCTR1) with S. inversa using the homologous cloning and RACE technology, and by means of sequence analysis, phylogenetic analysis, expression analysis and subcellular location analysis, explored the function of the gene and its aerenchyma. The results indicated that: (1) the ShCTR1 gene cDNA was 2 891 bp (NCBI accession number: ON081649) and contains 2 550 bp open reading frame encoding 849 amino acids, the theoretical isoelectric point is 5.90, with the molecular formula C₄₀₆₆H₆₄₁₇N₁₁₅₉O₁₂₆₈S₄₃. It was a hydrophobic protein with no transmembrane structure. (2) Phylogenetic tree analysis showed that S. inversa ShCTR1 had high similarity with CcCTR1 of Cynara cardunculus L., Sequence analysis of non-coding regions identified ShCTR1 containing a large number of photoresponse elements, suggesting that ShCTR1 may be involved in the response to UV stress. (3) Quantitative real-time fluorescence analysis showed that ShCTR1 were expressed in roots, stems and leaves, with the highest expression in roots, and its expression was upregulated under UV, cold and hypoxia stresses, which demonstrated that the ShCTR1 was involved in the response to the above three stresses. (4) Subcellular localization revealed that ShCTR1 was predominantly distributed in the nucleus. It had speculated that ShCTR1 may have an important role in the formation of aerenchyma as well as in response to adversity stress.