Understanding the resource allocation strategies of dominant conifer species in mountain forest ecosystem can provide decision-making basis for mountain ecosystem conservation and sustainable use. However, the resource allocation trade-offs of different tree species under the heterogeneous environments in arid and semi-arid mountains were not fully understood. Therefore, we analyzed the stoichiometric characteristics of two dominant conifer species in the Qilian Mountains at the eastern margin of the Tibetan Plateau with three altitudes and four typical regions to explore the resource allocation strategies of ecological adaptations of dominant tree species under different environmental gradients. The results showed that there were differences in stoichiometric characteristics for different tree species, altitudes and regions. 1) Compared with Qinghai spruce, Qilian juniper stored more nutrients in the underground part when it was resistant to drought. 2) Plants tended to invest more N and P to compensate for reduced physiological efficiency as altitude increases and temperatures decrease. 3) Different dominant conifer species stored more nutrients in the roots in the western section under drought stress. However, in the eastern section with favorable moisture and temperature they invested nutrients in the leaves and stems. 4) Mean annual temperature (MAT), mean annual precipitation (MAP) and soil water content (SWC) were the common controlling factors affecting stoichiometric characteristics of the different tree species, altitudes and regions. The findings of this study provided a theoretical basis for understanding of plant adaptation mechanisms at different spatial and temporal scales and species effects, as well as technical support for forest ecological control and restoration in ecologically sensitive and fragile areas.