Tree growth in the mid-latitudes of the northern hemisphere reveals significant inter-annual variation in carbon sequestration, and the variations have been widely attributed to climate change, especially to the recent rapid warming and increasing drought stress. However, the response of natural trees under the different regions that exist in the northeastern Qinghai-Tibetan Plateau remains unclear. Here, we use 9 Qilian juniper (Sabina przewalskii) tree-ring width and basal area increment (BAI) chronologies from the middle of the Qilian Mountains and the northeastern Qaidam Basin to quantify tree growth trends and their response to the recent rapid warming. The trees, growing at high and low elevations, exhibited a consistent pattern of inter-annual variations, with increasing synchronicity in their trends since 1950. Responses to several climate factors indicate that increasing temperature accelerated tree growth in the middle of the Qilian Mountains, but restricted tree growth in the northeastern Qaidam Basin. Moving-window correlation analyses demonstrate a clearly contrasting response to the temperature variations. Our findings suggest that growth of Qilian juniper in the middle of the Qilian Mountains will increase steadily in the future rapid warming, but may remain constant or even decrease in the northeastern Qaidam Basin. These contrasting responses to temperatures provide valuable information on forest dynamics in the critical mid-latitude regions that should be incorporated into predictions of future forest carbon cycling under global warming.