Rhododendron, a globally important group of alpine flowering plants, provides an exceptional system for investigating ecological adaptation and stress resistance owing to its high-altitude specialization. Using 18 Rhododendron species, a graph-based pangenome was constructed that captures 72,089 nonredundant structural variants. The findings support the integration of subgenus Azaleastrum into subgenus Tsutsusi, with their comparatively smaller genome sizes likely resulting from the contraction of multiple gene families during lineage differentiation. Gene families specific to high-altitude Rhododendron species were significantly enriched in pathways associated with stress resistance. High-altitude-specific long terminal repeat retrotransposons operate through similar regulatory mechanisms, predominantly influencing stress-responsive genes and promoting adaptive evolution. Through an integrated analysis of population genetics (389 re-sequenced samples with a mean coverage of 50.2×), transcriptomics, and real-time quantitative polymerase chain reaction, conserved genes and gene families linked to alpine adaptation in Rhododendron were identified. These include genes implicated in cold-stress responses and ultraviolet (UV) tolerance, such as CML18, CPK1, DREB1E, LPAT2, GPC1, and UVR8. Structural variant profiles within several of these genes offer insights into divergent adaptive mechanisms between high- and low-altitude Rhododendron species. The rapid induction of cold-sensing genes and CBF/DREB1-centered cold-stress signaling pathways indicates an evolutionary adaptation of alpine Rhododendron species to low-temperature habitats. Furthermore, transgenic analyses indicate that cold-resistance genes, such as GPC1 derived from high-altitude Rhododendron, markedly improve cold tolerance in Arabidopsis thaliana and tobacco. Collectively, this study advances insights into high-altitude adaptation in ornamental plants and underscores the value of super-pangenome resources for evolutionary and functional genomics research.