The physical and chemical characteristics of soil and water sources affect desert plants’ growth, which is essential for the ecological protection in arid areas. The typical patch patterns of Haloxylon ammodendron in the oasis-desert ecotone in the southern margin of the Manas River Basin consists of bare patches (BP) and vegetation patches (VP). The water sources of H. ammodendron were studied using stable isotope technology, and the soil physical and chemical properties were monitored and analyzed. The results showed that the soil moisture presented a reversed “S” type curve, and the total salt content of the soil presented an “S” type curve. A “wet island” and “cold island” were formed in the low salt area with H. ammodendron at the center. NaCl was most abundant in the BP soil, and the milligram equivalent of Cl− was 80–90%, while CaSO4 was most abundant in the VP soil, in which the milligram equivalent of SO42− was 80–100%. Before the rain, H. ammodendron mainly relied on the soil water from a deeper layer (≥60 cm) to maintain its growth. However, after the rain, H. ammodendron mainly relied on shallow soil water (<60 cm) to maintain its growth.