This paper aims to investigate the coordination and response mechanism of non-structural carbohydrate (NSC) content and its hydraulic characteristics in various organs of F. suspensa seedings during a prolonged period of drought stress. We exposed F. suspensa seedings to various degrees of drought treatments (CK, appropriate water supply; MS, moderate drought stress; and SS, severe drought stress) for three consecutive years. The changes in photosynthetic characteristics, the accumulation of biomass, the distribution of NSC, and the function of hydraulics in the various organs were measured under a prolonged period of drought stress. The carbon-water coordination of those indicators was also discussion in this paper. The results found that: (1) the 'native’ embolism of branches was 30.7%, 41.8% and 42.3%, respectively, under appropriate water supply, moderate drought stress, and severe drought stress. While the hydraulic conductivity of branches was 0.95, 0.71 and 0.65kg m^-1 s^-1 MPa^-1, respectively. (2) The net photosynthetic rate, transpiration rate, stomatal conductance, and water usage efficiency were all dramatically decreased after a prolonged period of severe drought stress. (3) Under severe drought stress, the fine root biomass and the root-to-shoot ratio significantly increased, while aboveground and coarse root biomass decreased significantly. In addition, the content of NSC each organ decreased significantly, with the highest NSC consumption in root system. The total soluble sugar and starch content of the root system significantly dropped, while the total soluble sugar glucose and sucrose content of the branches significantly increased by 12.9%, 31.1% and 45.7%, while the starch content significantly decreased by 40.7%. (4) The 'native’ embolism and hydraulic conductivity of branches was significantly correlated with the content of total soluble sugar, starch, sucrose, and glucose content (P ＜ 0.01), and the 'native’ of embolism of branches was a significant positive correlation with total soluble sugar, glucose, and sucrose content. In additional, there was a significant negative correlation with starch content (P ＜ 0.01). In conclusion, F. suspensa branches maintained lower hydraulic conductivity photosynthetic characteristics and hydraulic transport efficiency due to higher 'native’ embolism in the xylem of F. suspensa branches under long-term severe drought stress. Meanwhile, F. suspensa significantly increased the content of total soluble sugar, glucose, and sucrose content in the branches, while the starch and NSC content significantly decreased in response to improve the survival probability of plants under severe drought conditions and post-drought water recovery ability. This research provided a theoretical foundation for the cultivation and management of F. suspensa in semi-arid areas.