Qinghai spruce (Picea crassifolia) is the endemic tree species in the northeastern margin of the Qinghai-Tibet Plateau (QTP) in China. It plays an important role in maintaining ecological balance, biodiversity, and soil and water conservation in northwestern China. In this study, the current potential distribution of Qinghai spruce and its dominant climatic factors were analyzed firstly based on 69 distributional records via the maximum entropy model (Maxent). Then the distribution patterns of Qinghai spruce under three climate change scenarios (i.e., the lowest, a moderate, and the highest greenhouse gas emission scenarios; RCP2.6, RCP4.5 and RCP8.5) with three general atmospheric circulation models were predicted by Maxent for two future decades:the 2050s and 2080s. The results showed that the accuracy of the Maxent model was pretty high for modeling potential distribution regions of Qinghai spruce, and the average values of the area under the receiver operator characteristic curve (AUC) were higher than 0.99. The results from the Jackknife test and climate factor response curves revealed that the annual lowest precipitation is the key factor that limited the distribution of Qinghai spruce; the current potential distribution regions of Qinghai spruce are mainly concentrated in eastern Qinghai, southeastern Gansu, most of Ningxia, eastern Tibet, mountainous areas of western Sichuan, and parts of Shaanxi, Xinjiang, and Inner Mongolia. The total potential distribution area of Qinghai spruce in the 2050s and 2080s was changed little compared to the current distribution in all three scenarios, but its potential distribution area at different levels of fitness was changed a lot. Among them, the regions with fitness of less than 0.1 and in the range of 0.1-0.3 were significantly affected by the climate changes, and their area was largely increased in the medium emission scenario. In contrast, the regions with fitness in the range of 0.5-0.8 were shrunk in all scenarios. At the same time, the distribution patterns of Qinghai spruce in the 2050s and 2080s had a tendency to move northward in all scenarios, whereas its central distributional regions (more suitable regions) were still kept in eastern Qinghai and northern Gansu, with no obvious trend to change. From the perspective of climatic factors, this study showed that Qinghai spruce would continue to have important economic values and ecological service functions in the western mountains, especially in the Qilian Mountains and Helan Mountains, which are the important ecological barriers in China.