Water is not only an important factor limiting the survival and growth of plants, but also a factor influencing the distribution and quantity of vegetation in arid areas. Haloxylon ammodendron is a dominant plant species in the Gurbantünggüt Desert. Researching the water use pattern and seasonal changes is vital for understanding plant adaptation to environmental changes in the arid zone. In our study, the oxygen sable isotope ratios (δ18O) of xylem water and soil water in different soil layers (0—400 cm) were measured, and the water resource of young Haloxylon ammodendron in spring and summer were analyzed with direct comparison method, Iso-Source model and the mean depth of water uptake model. The results show that: (1) surface soil moisture (0—70 cm) in May was significantly higher than the surface soil moisture content in July, the difference of soil moisture content in 70—400 cm soil layer is not significant in Spring and Summer. (2) The δ18O values of surface soil water changed widely. In May, the δ18O value of surface soil water was varied and it’s significantly more negative compared with July. In July, the δ18O value of soil water gradually decreases with depth increases. (3) The mainly water resource of young Haloxylon ammodendron is the soil water in 0—50 cm soil layer in May, the use ratio is up to 67.5%. However, in July, the contribution of surface soil water decreased drastically while that deep soil water increased rapidly, the mainly water resource is the soil water in 250—400 cm soil layer in July, the use ratio is up to 94.2%.