Non-structural carbohydrates (NSC) affect tree growth and survival when photosynthesis is impacted by climate change, such as seasonal drought and extreme precipitation. Nevertheless, it is still unclear whether Eucalyptus suffers growth limitation under natural conditions and if trees recover under artificial cultivation. In present study, we conducted a field control experiment to compare the NSC storage in Eucalyptus urophylla × Eucalyptus grandis trees on fertilization and dry-season irrigation to determine the variations of NSC under drought stress. The results indicated total soluble sugar (TSS) was the primary existing form of NSC. In spatial patterns, NSC concentration showed gradient differences from source organ to sink organ, and finally accumulated in root. The TSS concentration showed a decreased trend with height except leaf, while the trend of starch concentration was contrast. Surprisingly, fertilization and dry-season irrigation had not changed the carbon distribution among all tissues but reduced the TSS concentration in most organs. The fast-growing E. urophylla × E. grandis will consume the assimilates and carbohydrates of storage organs, but maintains the NSC concentration at a certain threshold. Our results help to comprehend the NSC allocation and improve the productivity of E. urophylla × E. grandis plantations in seasonal arid areas.