Abstract This study presents an analysis of leave and rood morphology, biochemical and proteomics approach as adaptation strategies of the alpine plant Potentilla saundersiana in an altitude gradient. Several plant physiological parameter, including root and leaf architecture, leaf photosynthesis capacity, specific leaf area (SLA) and leaf nitrogen concentration, histology and microscopy, anthocyanin and proline contents, antioxidant enzyme activity assay, in-gel enzyme activity staining, H2O2 and O2− content, immunoblotting, auxin and strigolactone content and proteomics analysis were evaluated at five different altitudes. P. saundersiana modulated the root architecture and leaf phenotype to enhance adaptation to alpine environmental stress through mechanisms that involved hormone synthesis and signal transduction, particularly the cross-talk between auxin and strigolactone. Furthermore, an increase of antioxidant proteins and primary metabolites as a response to the alpine environment in P. saundersiana was observed. Proteins associated with the epigenetic regulation of DNA stability and post-translational protein degradation was also involved in this process. Based on these findings, P. saundersiana uses multiple strategies to adapt to the high-altitude environment of the Alpine region. Biological significance The alpine environment, which is characterized by sharp temperature shifts, high levels of ultraviolet radiation exposure, and low oxygen content, limits plant growth and distribution. Alpine plants have evolved strategies to survive the extremely harsh conditions prevailing at high altitudes; however, the underlying mechanisms remain poorly understood. The alpine plant Potentilla saundersiana is widespread in the Northwestern Tibetan Plateau. Here we adopted a comparative proteomics approach to investigate the mechanisms by which P. saundersiana withstands the alpine environment by examining plants located at five different altitudes. We detected and functionally characterized 118 proteins spots with variable abundance. Proteins involved in antioxidant activity, primary metabolites, epigenetic regulation, and protein post-translational modification play important roles in conferring tolerance to alpine environments. Furthermore, our results indicate that P. saundersiana modulates the root architecture and leaf phenotype to enhance adaptation to alpine environmental stress. These results provide novel insight into the multiple strategies underlying P. saundersiana adaptation to the high-altitude environment of the Northwestern Tibetan Plateau.