Non-structural carbohydrates’ (NSCs) allocation pattern is closely related to environmental factors, plant metabolism, and xylem function. At the same time, we know little about whole-tree NSC allocation patterns in different seasons, especially the high-elevation species which suffer from environmental stress. We examined the concentration of NSCs in various parts of Faxon fir trees (needles, branches, trunks, and roots) at five elevations (2800 m, 3000 m, 3200 m, 3400 m, and 3600 m) over four months (July 2019, October 2019, January 2020, and April 2020). The goal was to understand how NSC allocation patterns vary by location and time in high-elevation species and what factors contribute to these variations. The results showed that the needles had the highest concentration, followed by roots, branches, and trunks. The NSC concentration was highest in January 2020 and lowest in July 2019. The total non-structural carbohydrates (TNSCs) and soluble sugar concentrations of roots and needles were substantially higher in the cold (non-growing season) than in the warm (growing season) season. At different elevations, the soluble sugar concentrations in the needles and trunks remained the highest and lowest, respectively. Branches and roots’ soluble sugar concentrations alternated and varied with the seasons at all elevations. Many factors, such as climate, morphological traits, and carbon content, affected the spatial and temporal patterns of non-structural carbohydrates, with temperature, plant moisture conditions, and carbon content being the main driving factors. Various factors’ interaction mainly influenced NSCs’ spatial and temporal patterns. Non-structural carbohydrates significantly improve the resistance of Faxon fir trees’ terminal organs in adverse environments.