A global climate model has predicted changes in precipitation patterns, with extended periods of time between precipitation events; larger individual precipitation events are expected to increase. Furthermore, with global climate change, local area rainfall patterns have also changed. Over 80 years, the annual precipitation in arid areas of central Asia has generally shown an increasing trend. Such an altered precipitation regime will significantly alter the temporal supply of water to desert ecosystems, and thus have important effects on ecological processes, which could ultimately affect species composition and biological diversity. Root growth of seedlings is the most important stage in plant regeneration and the most sensitive in the plant life cycle to environmental conditions. The responses of root morphology to changes in precipitation and the ability of seedlings to adapt can directly affect the success of subsequent seedling establishment, and may affect regeneration dynamics. Nitraria tangutorum, a super-xerophytic shrub, exhibits a strong tolerance for drought, cold, and saline-alkali soil. The shrub vegetation type in which N. tangutorum is the dominant species is an important vegetation type in the deserts of northwestern China. As a result, N. tangutorum is the key species for the revegetation of these arid and semiarid areas. Most research has examined the impacts of the amount of precipitation on this species rather than the effects of both the amount and interval of precipitation. To understand how climate-driven changes in precipitation can affect desert plants, especially the response of the root morphology to precipitation patterns change, we conducted a controlled experiment with two factors: precipitation quantity (natural precipitation as a control, reduction of 30% and increase of 30%) and interval (time elapsed between two precipitation events; 5 or 10 days). The results showed that root morphological characteristics were influenced by total precipitation and precipitation interval, the former playing a more significant role than the latter. Under the same precipitation condition, the main root length, root diameter, root volume, and root surface area were decreased, total root length, root biomass, and total biomass were increased by extended precipitation intervals, and specific root length (SRL) and specific root area (SRA) were considerably increased by 45.09% and 20.20% in high precipitation, respectively, but the difference was not significant. For the same precipitation condition interval, the main root length was increased by 12.06%, total length, diameter, volume and surface area were significantly decreased, and SRL and SRA were basically unchanged in precipitation reduced by 30% conditions. The SRA increased significantly, but the other index differences were not significant. The main root length and root-shoot ratio were largest in low precipitation, but others (total root length, root surface area, average root diameter, root volume, root biomass, SRL and SRA) were larger in high precipitation conditions. Eight characteristics of root morphology were analyzed using principle component analysis. The characteristics of root biomass, total root length, total root surface area, SRL, SRA and root volume were significantly affected by precipitation pattern changes. We suggested that the root morphology of N. tangutorum seedlings was mainly affected by the amount of precipitation. However, the precipitation interval could be as important as the amount of precipitation for the root morphology of N. tangutorum seedlings. Increasing the precipitation amount and extending the precipitation interval (less frequent but higher volume precipitation events) enhanced root growth and population regeneration.