Abstract Analysis of water source and moisture transfer characteristics of desert plants is of great significance for ecological restoration in arid areas. In this study, the water source utilized by the desert plant, Haloxylon ammodendron, was analysed using the stable isotope technique, and the water transportation characteristics were obtained based on the proportional heat balance method under different weather conditions. The results showed that (1) before raining, the moisture of H. ammodendron mainly relied on groundwater (the average contribution rate was 34.14%) and on soil water located at a depth of 120–180 cm (the average contribution rate was 29.87%). After the rain, H. ammodendron mainly absorbed soil water from a depth of 60–120 cm (the average contribution rate was 33.19%) and groundwater (the average contribution rate was 30.67%); (2) the stem flow of H. ammodendron showed an obvious diurnal variation, showing a “midday rest” phenomenon. The stem flow showed a peak value, and in sunny days, it was ~2 fold higher than that in cloudy days. (3) The stem flow rate of H. ammodendron varied regularly overtime as follows: August > July > September > June > May, and the meteorological factors affecting its stem flow were solar radiation (0.826) > atmospheric temperature (0.598) > humidity (-0.573). The results provide basic support for the ecological conservation of the desert plant H. ammodendron, while also having important implications for ecological restoration in arid regions.