Stipa purpurea is widely distributed along a large precipitation gradient on the Tibetan Plateau. This implies that S. purpurea from different populations may have different responses to drought stress. To explore this we compared the morphological and physiological changes of S. purpurea seedlings cultivated from seeds from Gar County and Nagqu County after 7 and 14 days of drought stress and subsequent re-watering. The results showed that S. purpurea plants from the more arid Gar area were more tolerant to drought stress than that from Nagqu. To investigate the potential mechanisms underlying this difference, we used iTRAQ quantitative proteomics technology to analyze protein dynamics in S. purpurea samples treated with 7 days of drought stress and subsequent re-watering. The results indicated that, during the process of drought and re-watering treatments, there were differentially expressed proteins in either or both S. purpurea populations. These differential proteins were divided into 24 functional categories that were mainly associated with stress response, the antioxidant system, photosynthesis, carbohydrate metabolism, and post-translational modifications. According to these results, we concluded that the molecular basis of stronger drought resistance likely lies in the specific up-regulation or higher expression of many proteins involved in stress response, the antioxidant system, post-translational modification and osmotic regulation in S. purpurea from Gar County compared with that from Nagqu. This study improves our understanding of the intraspecific differences in drought resistance within S. purpurea populations, which helps to understand the distribution of S. purpurea along the moisture gradient, as well as the effect of climate change on this species.