This study explored the physiological response mechanism of alfalfa seedlings roots to a typical explosive, cyclotrimethylenetrinitramine (RDX), so as to improve the efficiency of phytoremediation. The response of plants to different levels of RDX were analyzed from the perspectives of mineral nutrition and metabolic networks. Exposure to RDX at 10–40 mg L−1 had no significant effect on root morphology, but the plant roots significantly accumulated RDX in solution (17.6–40.9%). A 40 mg L−1 RDX exposure induced cell gap expansion and disrupted root mineral metabolism, The key response elements, P, Cu, and Mg, were significantly increased by 1.60–1.66, 1.74–1.90, and 1.85–2.50 times, respectively. The 40 mg L−1 RDX exposure also significantly disturbed root basal metabolism, resulting in a total of 197 differentially expressed metabolites (DEMs). The main response metabolites were lipids and lipid-like molecules, and the key physiological response pathways were arginine biosynthesis and aminoacyl-tRNA biosynthesis. A total of 19 DEMs in root metabolic pathways, including L-arginine, L-asparagine, and ornithine, were significantly responsive to RDX exposure. The physiological response mechanism of roots to RDX therefore involve mineral nutrition and metabolic networks and are of great significance for improving phytoremediation efficiency.