Cadmium (Cd) pollution significantly hampers cleaner production of peanut (Arachis hypogaea L.). Therefore, exploring of tolerance mechanisms to Cd stress and breeding of low-Cd peanut cultivars are urgently needed and require intense efforts. Herein, multi-omics and physiological studies reveal that multiple biological processes, including melatonin (MT) biosynthesis, are involved in the Cd tolerance in peanut plants. Exogenous MT was applied to peanut plants under Cd stress, which decreased Cd accumulation in roots, shoots and seeds for 40%-60%, and promoted the antioxidant capacity. Integrated investigation reveals that MT-mediated Cd tolerance is mainly attributed to the enhanced metabolism of linolenic acid, glutathione (GSH), and phenylpropanoid (lignin), and development of casparian strip in root cell wall. Defense genes, such as non-race-specific disease resistance gene 1/harpininduced gene 1 (NDR1/HIN1)-like in peanut (AhNHL), were also significantly upregulated by MT under Cd stress. Overexpression of the AhNHL gene in tobacco reduced Cd accumulation for 37%-46%, and alleviated photosynthesis-inhibition induced by Cd stress. Transcriptomic analysis suggested that AhNHL confers the Cd tolerance mainly through promoting phenylpropanoid biosynthesis and GSH metabolism. Additionally, exogenous GSH effectively alleviated the Cd stress through improving Cd sequestration and antioxidant capacity in peanut plants, while apply of the GSH biosynthesis inhibitor (buthionine sulfoximine) exacerbated the Cd phytotoxicity. Transcriptomic analysis reveals that exogenous GSH improves Cd tolerance through affecting the expression of genes involved in transcription regulation, and metal ion binding and transport. Our findings provide novel insights into molecular mechanisms underlying Cd tolerance in plants, which would facilitate breeding of low-Cd peanut cultivars.