Tsuga longibracteata is a unique, precious, relic tree species in China, which has been used for afforestation, as well as timber and medicine. Further, the plant is worth studying because it is important in the study of phylogeny of gymnosperms, paleoecology, and the Paleoclimate. Predicting changes in suitable distribution areas of Tsuga longibracteata under climate change scenarios are an important basis for formulating its conservation and development strategy. In this study, the Maximum Entropy Model (MaxEnt) was used to explore the relationship between climate change and the geographical distribution of the species in different time periods (current, 2050, and 2070) and carbon dioxide emissions (RCP2.6 and RCP8.5), to predict the changes in the suitable distribution areas of Tsuga longibracteata. In addition, the spatial constraints on species distribution were considered, and the climate factor prediction model (C) and climate + spatial constraint factor prediction model (C+S) were respectively used to predict the changes in potential distribution areas of the tree. The results showed that the precipitation for the driest month and the annual temperature range were the dominant climatic factors affecting its geographical distribution with spatial constraints on having some important influences. With the increase in time, the total suitable distribution area of the tree was reduced, especially the most and more suitable distribution areas decreased greatly and shifted towards the north, which were more prominent trends in RCP 8.5 scenario. Our findings indicated that future climate change may lead to shrinkage of the Tsuga longibracteata population and decreased its suitable habitat area; thus, increasing threats to its population. On adding the space constraint factor in the model, the prediction accuracy of the C+S model was higher, and the results more strongly fit with the migration and diffusion characteristics of the tree. The core distribution area in the future was still located at the junction of the three provinces in Hunan, Guangxi, and Guizhou, where the tree is currently distributed, indicating the junction is a refuge place for the tree in the future climate changes. In addition, the Daba mountain area in combination with the Chongqing, Sichuan, and Hubei are the theoretical distribution area of Tsuga longibracteata in the future under climate change. They can be used as new introduction culture areas of the tree under the future climate change. The results provided a scientific basis for the conservation and sustainable management of the species in the context of the climate change, and a case integrating spatial constraint into a climate model for species distribution prediction, which will benefit accurate prediction of the geographical distribution of endangered and rare plants.