Climate change is considered to affect the species distribution deeply in time and space. Knowledge of how plant distribution responded to climate change may help us know their evolutionary history and predict ongoing environmental changes. Elevational range shifts of species in response to climate change is a common phenomenon in mountains, especially for the closely related species in sympatric. Here, we selected Taxus chinensis and Taxus mairei to explore this issue. Four types of environmental variables were used to simulate the distribution patterns, under the historical climate and future climate change scenarios, with the optimization Maxent model. We found that elevational distribution of two species has significant differences. The distribution of T. chinensis was higher than that of T. mairei. The centroid of T. chinensis and T. mairei were in Sichuan and Hunan province, respectively. Temperature and precipitation were the main factors that determine the potential distribution of the two species, and the suitable distribution area of T. chinensis was lower than T. mairei. In the future, the direction of centroid migration of two species was almost opposite, T. chinensis will shift southwest while T. mairei go northeast. Our results not only provided an insight to discriminate two sympatric species in subtropical and warm temperature zones, but also gave us an important reference for the conservation of these valuable endangered species.