Allium mongolicum Regel is a desert plant that shows great resistance to wind erosion, drought, and low temperatures and is widely distributed in the desert lands of China. Understanding the molecular mechanisms underlying its drought resistance is essential for uncovering drought resistance genes and improving its beneficial traits. Here, a de novo RNA-Seq assembly analysis was conducted using the roots of 1-month-old seedlings under drought stress. Using pairwise comparisons of untreated plants (CK), 48-hour drought plants (G48h), and 96- hour drought plants (G96h), in total, 2,211 differentially expressed unigenes (DEGs) were obtained. Furthermore, using functional annotation, these DEGs were mainly involved in the plasma membrane, photosynthesis, and secondary carbohydrate metabolism. Moreover, genes involved in the ABA-mediated signaling pathway and secondary metabolism were upregulated in the roots. These results suggest that desert plants may use signaling and secondary metabolic pathways as adaptive responses to drought stress. Collectively, this work could help elucidate the molecular mechanisms underlying the ability of A. mongolicum Regel to respond to drought stress and aid in the selection of novel drought tolerance genes.