Significant increases in the concentration of carbon dioxide (CO₂) have been shown to cause changes in precipitation patterns. These changes can severely affect the desert ecosystem. Therefore, it is important to investigate the impacts of CO₂ concentration and precipitation on root morphology, so as to better predict the responses of desert ecosystems to the global climate change. For this purpose, we studied Reaumuria soongorica that is a dominant plant in the desert. Open top chambers were used to simulate changes in CO₂ concentrations (350 μmol mol⁻¹ and 700 μmol mol⁻¹), to study the effects of 30% reduction in precipitation (W−), natural precipitation (W), 30% increase in precipitation (W+), and to study the synergistic effects of precipitation with CO₂ on R. soongorica root morphological characteristics, endogenous hormones, and soluble sugars. Higher CO₂ levels caused a significant increase in root length, mean root diameter, root biomass, total root surface area and total root volume regardless of alterations in precipitation; whereas the root–shoot ratio increased only with increased precipitation. Elevated concentrations of CO₂ and decreased precipitation significantly increased the contents of fructose, sucrose, glucose and other soluble sugars in the R. soongorica root system. Meanwhile, the two environmental factors showed significantly synergistic effects on R. soongorica root morphology. With elevated concentrations of CO₂, R. soongorica roots showed increased levels of endogenous hormones, including abscisic acid (ABA), indole-3-acetic acid (IAA) and gibberellin (GA). The effect of precipitation on hormone levels varied among hormones. IAA and GA levels were increased, regardless of changes in precipitation; ABA decreased with higher precipitation, whereas zeatin (ZT) increased with more precipitation. Correlation analyses indicated a significant correlation between root morphology and the levels of soluble sugars and endogenous hormone, as well as between the level of soluble sugars and the level of endogenous hormones. We conclude that future changes in climate conditions such as CO₂ levels and precipitation will synergistically induce the root system of R. soongorica to undergo morphological and physiological alterations.