Under the influence of global climate and land use changes, the distribution of many species has undergone alterations. Being classified as a third-level national key-protected wild medicinal species in China, there is a knowledge gap regarding the distribution changes of Gentiana scabra Bunge under the influence of these factors. In order to elucidate how G. scabra is impacted by climate and land use changes, this study developed the current and future potential distribution of G. scabra using the BIOMOD2 R Package and three dispersal scenarios. By integrating global future land use data, we analyzed the impact of land use changes on G. scabra natural habitats and clarified the differences in habitats of varying suitability areas. Subsequently, utilizing the landscape fragmentation layer calculated by Fragstats software, we identified priority conservation areas and analyzed the conservation gap. Additionally, the MuMIn R Package was employed to examine the relationship between environmental variables and the content of the active ingredient gentiopicroside. Subsequently, layers depicting the content of gentiopicroside under current and future climatic conditions were developed. These layers serve as the foundation for planning high-quality wild tending areas under the influence of climate and land use changes. Consequently, a conservation plan for G. scabra within China was formulated. The results indicate that, influenced by climate and land use changes, the populations experience both the opportunity of an expanding potential distribution and the crisis of diminishing high natural habitats annually in the future. In China, the currently protected areas cover a mere 0.25% of the current potential distribution, which is insufficient for safeguarding the wild resources of G. scabra. Specific conservation recommendations were proposed based on these results to counteract the escalating threat and ensure the continued growth of the wild population of G. scabra. This study contributes to the conservation and restoration of G. scabra's wild resources and introduces a novel idea for the conservation of other rare and endangered species.