Abscisic acid (ABA) has been well known to strongly improve plant tolerance to heavy metals. However, the comprehensive mechanism of alleviating cadmium (Cd) stress in different plant organ was not been fully elucidated. In this study, foliar spray of 10 μM ABA significantly (p < 0.05) improved the plant height, root length, and the number of lateral roots, and reduced Cd accumulation and effectively restored the mineral contents caused by Cd induced change in leaves, stems, and roots of mung bean seedlings. Transcriptome analysis revealed that a total of 2241 differentially expressed genes (DEGs) (|fold-change|≥ 2.0 and FDR ≤ 0.05) were identified in the ABA + Cd-treated mung bean seedlings compared to the Cd-treated group, with 898, 908, and 859 DEGs identified in leaves, stems, and roots, respectively. Foliar application of ABA predominantly affected the KEGG pathways including phenylpropanoid biosynthesis, alpha-linolenic acid metabolism, starch and sucrose metabolism, and cyanoamino acid metabolism, and regulated the genes related to lipid metabolism, cell wall processes, secondary metabolism, defense and stress responses, hormone signal transduction, photosynthesis, and cell division to mitigate Cd toxicity of the mung bean seedlings. However, ABA exerted distinct effects on the gene profiles of leaves, stems, and roots under Cd stress. Interestingly, although exogenous ABA was applied to the leaves, the genes involved in hormone signaling were found to be regulated primarily in roots on the first day and subsequently in stems and leaves at later stages, indicating that exogenous ABA participates in mitigating Cd toxicity through signal transduction. Notably, significant upregulation of transporter-related genes was observed mainly in leaves and stems, including ABC transporters, NRT1/PTR FAMILY protein encoding genes, and WAT1-related protein encoding genes, which may contribute to the transportation of the ABA, Cd, and nutriments. Furthermore, the expression of genes encoding crucial photosynthetic proteins exhibited significant upregulation or downregulation upon exogenous ABA treatment, implying that exogenous ABA also ameliorated Cd stress by modulating leaf photosynthetic activity. This study may contribute to understanding the molecular mechanism of ABA-alleviated Cd stress in mung bean and identifying a number of highly regulated genes that could potentially be used to improve plant tolerance to heavy metals. [ABSTRACT FROM AUTHOR]