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Rhodiola linearifolia Boriss., a perennial alpine plant from the Crassulaceae family, is renowned for its unique medicinal properties. However, existing research on this species is limited, particularly regarding the impact of altitude on its physiological and medicinal compounds. The current study employed morphophysiological and anatomical methods to explore the adaptive mechanisms of R. linearifolia across different altitudinal gradients, while also examining photosynthetic pigments and metabolomic changes. Our results indicate that despite the simultaneous effects of various mountain abiotic factors, significant correlations can be identified between altitude and trait variation. An optimal growth altitude of 2687 m above sea level was identified, which is pivotal for sustainable ecosystem management and potential species introduction strategies. It is noted that increasing altitude stress enhances the synthesis of secondary antioxidant metabolites in R. linearifolia , enhancing its pharmaceutical potential.