As climate change and human activities continue to influence the environment, the area of arable land has been decreasing and becoming more susceptible to the impact of salt ions. Consequently, understanding the molecular mechanisms behind hydrogen's mitigation of plant salt tolerance is essential. In this study, strawberries were selected as the test plants, and analyses including physiological, biochemical, transcriptomic, and metabolomic approaches were conducted to elucidate the effects of hydrogen-rich water (HRW) under salt stress. The results indicated that under 100 mM salt stress, HRW significantly promoted plant growth, particularly increasing root biomass by 49.50%. Additionally, HRW regulated the levels of soluble sugars, malondialdehyde (MDA), and antioxidant enzymes, enhancing the cellular uptake of potassium ions and the expulsion of sodium ions. The levels of Ca2+ and Mg2+ in organelles increased by 2.06 and 2.45-fold, respectively. Transcriptomic analysis revealed that HRW substantially altered gene expression in strawberry roots; under salt stress, HRW up-regulated beneficial biological processes. Furthermore, genes related to ion absorption and transport, antioxidant enzymes, and cell wall biosynthesis were screened. Through integrating transcriptomic and metabolomic analyses which identified key common pathways in the differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs) related to phenylpropanoid biosynthesis, alanine, aspartate, and glutamate metabolism, amino sugar and nucleotide sugar metabolism, and galactose metabolism. A molecular mechanism for mitigating salt stress in strawberry seedlings by HRW was provided by the integrated approaches in this research, reflecting the potential applications of hydrogen gas in agriculture.