Understanding the interaction between drought and ontogenetic stage or size of trees is an important research priority because the mortality pattern that depends on individual size of tree has an important impact on the structure and function of forest ecosystems. Haloxylon ammodendron, one of the widely distributed small trees in the southern margin of Gulbantonggute Desert, was taken as the target plant species in this study. We measured the predawn leaf water potential (Ψ_pd), PV curve, maximum stomatal conductance (G_s), maximum photochemical efficiency (F_v/F_m) of the H.ammodendron with different tree sizes (represent by basal stem diameter) during the growing season. To ascertain root distribution and rooting depth of different tree sizes, we carried out root investigation by digging method. The responses of different tree sizes surrogated by the basal stem diameters of H.ammodendron to drought were analyzed by combining gravimetric soil water content, plant physiological traits and rooting depth. Our results showed that summer drought stress significantly constrained the physiological traits performance of the small young trees with basal stem diameter of 0-1 cm and 1-2 cm, more than the larger adult trees with basal stem diameter of 4-8 cm and >8 cm. Compared with the adult trees, the Ψ_pd、F_v/F_m、osmotic potential at full turgor(π₁₀₀)、osmotic potential at turgor lost point(Ψ_TLP) of the young trees dropped significantly. Across the basal stem diameter groups, rooting depths were closely related to plant physiological traits. The contrasting physiological traits performance during the summer drought among the tree size groups of H.ammodendron was the result of the interaction between plant root distribution characteristics and the soil water conditions. Rooting depth dominated plant from which soil depth and corresponding soil volume to obtain water, and then determined the plant water status and thus the physiological response characteristics of different tree sizes during summer drought. Hence, rooting depth appeared to be a critical trait at the basis of tree resistance and resilience to extreme drought events and may be the most important traits defending trees with different size from drought-induced mortality. For the small young trees, their root systems were not fully developed (shallow rooting depth), which could only use the limited shallow soil water input by precipitation and thus was sensitive to drought stress. For the adult and older trees, their root systems were well developed and could fully use the deep soil moisture hence reduce the adverse effects of surface soil drying. Desert shrubs of different ages or sizes have different rooting depths and may experience different soil moisture environments. Further research should give more attention on how individuals of different sizes respond to and adapt to the contrasting soil water conditions.