Abstract: The encroachment of shrubs in desert grasslands exacerbates water consumption, leading to increasingly severe water scarcity in these regions. Determining appropriate shrub density is crucial for vegetation establishment and ecological restoration. However, the response of water use strategies in desert grassland shrub—encroached vegetation to different densities remains unclear. In this study, hydrogen and oxygen stable isotope techniques combined with a Bayesian mixing model (MixSIAR) were applied to analyze differences in water use strategies among Caragana korshinskii, Stipa breviflora, and Lespedeza potaninii. The results showed that: (1) Soil moisture content decreased with increasing planting density. The average soil moisture content in T1 (1200 plants/hm2) and T2 (1600 plants/hm2) was higher than that in T3 (2352 plants/hm2) and T4 (3076 plants/hm2). In the late growing season (August to October), the shallow soil moisture content in T1 was significantly higher than that in T3. (2) As the growing season progressed, significant differences in water sources from various soil layers were observed among the shrub—grass systems under different planting densities. In May and July, T1 and T2 preferentially utilized shallow soil water (0—40 cm), with absorption proportions ranging from 20.60% to 27.97%, while T3 and T4 relied more on middle and deep soil water (40—300 cm), with absorption proportions ranging from 20.23% to 23.53%. Stipa breviflora in T3 and T4 primarily depended on soil water from 0—20 cm, with absorption proportions ranging from 34.83% to 58.47%. (3) Short—term sufficient rainfall significantly altered plant water use strategies in the desert grassland shrub—grass system. In June and August, when precipitation was relatively high, Caragana korshinskii and Lespedeza potaninii mainly utilized shallow soil water. This study revealed the response strategies of plant water use to density in desert grassland shrub—grass systems, providing a theoretical basis and data support for the scientific allocation of shrubs in ecological restoration in this region.