Arbuscular mycorrhizal fungi (AMF) can develop a symbiotic relationship with the roots of most terrestrial plants, which can improve the drought tolerance of the host plants. Based on our previous studies, AMF play a critical role in promoting native plant growth in the arid valley of the Minjiang River, China. Furthermore, the effects of AMF on root growth are as important as their effects on aboverground growth. To understand how plant roots respond to AMF under different drought stress conditions, we designed a completely randomized full factorial pot experiment in a greenhouse in the arid valley of the Minjiang River. We added one common AMF (Funneliformis mosseae, FM) to the roots of seedlings from a dominant native shrub (Bauhinia faberi var. microphylla), using three different drought stress conditions. Continuous drought stress was induced by watering the seedlings with distilled water at one-day intervals for three months at low (40%), medium (60%), and high levels (80%) of the field capacity. At the end of the experiment, we harvested the seedlings, and cleaned their roots with distilled water. We subsequently measured the root fresh weight, scanned the roots with a root scanner (EPSON 11000XL), and obtained variables such as root length, root surface area, root volume, root forks, and number of root tips with WinRhizo. We subsequently analyzed the root architecture and the functional characteristics of the B. faberi seedlings to address the relationship between root development and AMF presence under different levels of drought stress. We used one-way ANOVAs, two-way ANOVAs, LSD fitting methods, and Pearson's correlations for our statistical analyses. Inoculation of FM significantly increased the total root length, root surface area, root forks, and the number of root tips under all three drought stress conditions (P < 0.001). In addition, under medium and high soil water content, it significantly increased root fresh weight and root volume (P < 0.001). More specifically, high soil water conditions resulted in the significantly highest root fresh weight, total root length, root surface area, root volume, and number of root tips after FM addition. Nonetheless, there was no significant difference in average root diameter between inoculated and non-inoculated seedlings. Inoculated seedlings tended to develop a dichotomous branching style, which was more profound at low (40% of field capacity) soil water content (P < 0.001). Furthermore, the root fractions of inoculated seedlings were significantly smaller than the non-inoculated seedlings (P < 0.001). However, there was no significant difference in specific root length among all the treatments. Root fresh weight, root length, root surface area, root volume, root forks, and number of root tips correlated significantly and positively with colonization rate (P < 0.001). In contrast, topological index and root fraction were significantly and negatively correlated with colonization rate (P < 0.001). Overall, we found that, although AMF did not improve the root absorption efficiency in the initial growth period of B. faberi, AMF presence significantly affected seedling root morphology and root functional characteristics. These latter effects enhanced B. faberi seedling growth, which allowed the plants to adapt to drought conditions. Finally, the positive effects of AMF on root growth increased with improving water conditions.