<p>Soil salinization is a predominant factor restricting plant growth and yield. In this study, common and salt-tolerant wild soybeans were treated with NaCl: Na₂SO₄ (1:1) at vegetative emergence stages. Salt tolerance metabolic regulatory modules of the cotyledons were determined by comparing differences in growth, physiology, metabolomics and transcriptomics. We found that salt-tolerant soybeans could maintain relative stability of cotyledon growth parameters and chloroplast microstructure. Additionally, they could sustain the stability of photosynthetic parameters and Ca²⁺ concentration, increase K⁺ content, and reduce Na⁺ accumulation through up-regulating related genes. The molecular interaction relationships between differentially expressed genes and differential metabolites revealed by association analysis indicate that the key metabolic regulatory mechanisms for salt tolerance in wild soybean cotyledons involve the enhancement of the daidzein biosynthesis pathway, loganin biosynthesis pathway, and the myo-inositol-ascorbate synthesis pathway within the secondary antioxidant metabolism module, as well as the strengthening of abscisic acid biosynthesis and metabolism pathways. Additionally, they involve the upregulation of osmotic regulation modules, including fructose-sucrose metabolism, fructose-mannose metabolism, maltose metabolism, and the tricarboxylic acid cycle. There results will help improve the physiological and biochemical theory of soybean and have important guiding significance for the breeding of new varieties of salt-tolerant soybean plants.</p>