Vegetation root water uptake plays a significant role in water transport processes and has multiple effects along the soil–vegetation–atmosphere interface, particularly in semi-arid and arid ecosystems. The objective of this study was to quantitatively examine the water uptake in Cynanchum sibiricum, a common desert rattan plant in arid regions, during its growth period, as well as to assess the relevance of the contributions of various water sources via a multivariate linear mixed model based on water-stable isotopes and eliminating the significant short-term impact of precipitation pulses on root water uptake. The results indicated that when the influence of a precipitation event was minimized, 0–10 cm soil water was the dominant water source for Cynanchum sibiricum in its growth phase, and that the species’ relative uptake of rainfall was positively proportional to that of 10–70 cm soil water while negatively proportional to that of 0–10 cm soil water. We concluded that Cynanchum sibiricum relies on its active roots extending transversely to extract water from shallow soil to survive under extreme drought conditions and would be inseparable from the symbiosis formed with other deep-rooted vegetation. Additional research into disentangling the water transport processes and studying the ecohydrological feedback along the soil–vegetation interface in arid ecosystems would be beneficial and could contribute to the evidence-based management of water resources for ecological protection.