In this experiment, we used the seedlings of the main constructive species of Reaumuria soongorica in the desert area as the experimental material, and set four different water treatments including suitable water (CK), light drought stress (MD), moderate drought stress (SD) and serious drought stress (VSD), i.e., 80%, 60%, 40% and 20% of the water holding capacity in the field. The contents of non-structural carbohydrates (NSC) and their components in leaves, stems, coarse roots and fine roots of R. soongorica seedlings at 15 d, 30 d, 45 d and 60 d of drought stress were measured by pot water control experiment. The dynamic changes and differences of components of NSC in R. soongorica seedlings under different stress intensities and drought durations were analyzed, aim to reveal the response mechanism of R. soongorica NSCs to drought stress. The results showed that: (1) the intensity and duration of drought stress had a significant effect on the NSC and their components of different organs in R. soongorica seedlings, and the duration of stress had a particularly significant effect on the dynamic changes of NSC. (2) In the early stage of drought stress, the NSC content in leaves of R. soongorica showed a downward trend, while the NSC content in stems showed an upward trend, and the NSC content in coarse roots and fine roots remained basically stable under various stress treatments. (3) In the late stage of drought stress, the soluble sugar, starch and NSC content in leaves and stems of R. soongorica gradually increased, while the starch and NSC content in coarse roots and fine roots showed a downward trend (except moderate drought stress), and during this period, the contents of soluble sugar and NSC in various organs under serious drought stress treatment is significantly higher than those of CK. The study found that severe drought stress could significantly induce the increase of NSC content in different organs of R. soongorica seedlings, and the balance of cell osmotic potential was regulated by decomposing starch in roots and increasing soluble sugar content in leaves to maintain cell vitality, thus maintaining the survival of R. soongorica in the late stage of drought stress.