Caraganajubata is a keystone species in high-altitude ecosystems, widely distributed across alpine regions above 2000 m in elevation. It demonstrates a strong adaptive capacity to extreme environments. The mechanisms that underlie the maintenance of its genetic diversity and its environmental adaptive evolution represent critical research directions in the conservation genetics of alpine plants. However, due to a lack of baseline information on its genetic diversity, the adaptive mechanisms of this species in heterogeneous habitats remain poorly understood. In this study, simple sequence repeat (SSR) primers were developed using simplified genome sequencing data to systematically investigate the patterns of genetic diversity and the environmental driving mechanisms of Caraganajubata. The results indicated low genetic diversity within natural populations, characterized by weak genetic differentiation (Gst = 0.1330) and frequent gene flow among populations (Nm = 3.2596). Population structure analysis revealed that the species could be divided into three genetic clusters, with their spatial distributions significantly correlated with altitudinal gradients. Additionally, environmental factor association analysis identified altitude as the primary factor influencing genetic diversity. This study elucidates the influence of altitudinal gradients on the genetic structure of alpine plants, offering genomic insights for developing biodiversity conservation strategies in cold-arid regions. The findings have significant implications for the protection and sustainable use of alpine plant resources.