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Desert phreatophytes are greatly dependent on groundwater, but how their root systems adapt to different groundwater depths is poorly understood. In the present study, shoot and root growths of Alhagi sparsifolia Shap. seedlings were studied across a gradient of groundwater depths. Leaves, stems and roots of different orders were measured after 120 days of different groundwater treatments. Results indicated that the depth of soil wetting front and the vertical distribution of soil water contents were highly controlled by groundwater depths. The shoot growth and biomass of A. sparsifolia decreased, but the root growth and rooting depth increased under deeper groundwater conditions. The higher ratios of root biomass, root/shoot and root length/leaf area under deeper groundwater conditions implied that seedlings of A. sparsifolia economized carbon cost on their shoot growths. The roots of A. sparsifolia distributed evenly around the soil wetting fronts under deeper groundwater conditions. Root diameters and root lengths of all orders were correlated with soil water availabilities both within and among treatments. Seedlings of A. sparsifolia produced finer first- and second-order roots but larger third- and fourth-order roots in dry soils. The results demonstrated that the root systems of desert phreatophytes can be optimized to acquire groundwater resources and maximize seedling growth by balancing the costs of carbon gain.