Rapid climate and land-use changes have been considered as the foremost threat to global biodiversity. China contains more than 3500 threatened higher plants, whereas the relative influence of climate and land-use changes on these endangered plants have not been explored simultaneously under topographical constraints. Here, using Taxus plants as the case study genus, we simulated the distribution range of threatened species under three scenarios of current and future climate and land-use conditions under topographical constraints. We also measured the associated difference in the responses of Taxus species to climate and land-use changes. Our results demonstrated the substantial influence of climate and land-use changes on the distributions of Taxus species. However, we observed different responses of Taxus species to these environmental changes. The distribution range of T. cuspidate Siebold & Zuccarini and T. mairei Lemee & H. Léveillé would substantially shrink, whereas the habitat range of T. fuana Nan Li & R. R. Mill would sharply expand under RCP 8.5(Representative Concentration Pathway scenarios) scenario. Meanwhile, T. wallichiana Zuccarini and T. chinensis (Pilger) Florin would experience apparent range shifts. Furthermore, topographical factors played non-negligible roles in shaping species distributions, and modifying the influence of climate and land-use changes. Together, these results provide robust evidence that even threatened species will have multiple responses to climate and land-use changes (e.g., shrinking, expanding, shifting). Our findings highlight that taking species ecological traits, habitat characteristics, and topographical constraints into account might provide valuable insights into threatened species conservation in the face of global environmental changes.