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Malus is an economically important plant that is widely cultivated worldwide, but it often encounters saline–alkali stress. The composition of saline–alkali land is a variety of salt and alkali mixed with the formation of alkaline salt. Hydrogen sulfide (H₂S) has been reported to have positive effects on plant responses to abiotic stresses. Our previous study showed that H₂S pretreatment alleviated the damage caused by alkaline salt stress to <i>Malus hupehensis</i> Rehd. var. <i>pingyiensis</i> Jiang (Pingyi Tiancha, PYTC) roots by regulating Na⁺/K⁺ homeostasis and oxidative stress. In this study, transcriptome analysis was used to investigate the overall mechanism through which H₂S alleviates alkaline salt stress in PYTC roots. Simultaneously, differentially expressed genes (DEGs) were explored. Transcriptional profiling of the Control-H₂S, Control-AS, Control-H₂S + AS, and AS-H₂S + AS comparison groups identified 1618, 18,652, 16,575, and 4314 DEGs, respectively. Further analysis revealed that H₂S could alleviate alkaline salt stress by increasing the energy maintenance capacity and cell wall integrity of <i>M. hupehensis</i> roots and by enhancing the capacity for reactive oxygen species (ROS) metabolism because more upregulated genes involved in ROS metabolism and sulfur-containing compounds were identified in <i>M. hupehensis</i> roots after H₂S pretreatment. qRT-PCR analysis of H₂S-induced and alkaline salt-response genes showed that these genes were consistent with the RNA-seq analysis results, which indicated that H₂S alleviation of alkaline salt stress involves the genes of the cell wall and sulfur-containing compounds in PYTC roots.