Kingdonia uniflorais an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position makeK. unifloraan ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals from three representative locations and adopted RNA-seq technology to sequence 18 tissues, aiming to uncover howK. unifloraresponded to different altitudes at the gene expression level. We revealed that genes that responded to light stimuli and circadian rhythm genes were significantly enriched in DEGs in the leaf tissue group, while genes that were related to root development and peroxidase activity or involved in the pathways of cutin, suberin, wax biosynthesis, and monoterpenoid biosynthesis were significantly enriched in DEGs in the flower bud tissue group. All of the above genes may play an important role in the response ofK. uniflorato various stresses, such as low temperatures and hypoxia in high-altitude environments. Furthermore, we proved that the discrepancy in gene expression patterns between leaf and flower bud tissues varied along the altitudinal gradient. Overall, our findings provide new insights into the adaptation of endangered species to high-altitude environments and further encourage parallel research to focus on the molecular mechanisms of alpine plant evolution.