ABSTRACT: Saline-alkali stress is a widespread abiotic stress that severely impairs crop growth and yield formation. Iron Chlorine e6 (ICe6), a novel plant growth regulator, has potential application value in promoting chlorophyll synthesis and enhancing stress resistance. In this study, soybean cultivars Henong 95 (HN95, salt-alkali-sensitive) and Hefeng 50 (HF50, salt-alkali-tolerant) were treated with foliar application of 120 nmol/L ICe6 at the R1 stage. SA treatment significantly inhibited soybean plants, as evidenced by decreased antioxidant capacity, massive reactive oxygen species (ROS) accumulation, and reduced photosynthetic pigment content when compared with the control (CK). This significantly reduced carbohydrate accumulation and ultimately decreased yield. ICe6 treatment significantly alleviated saline-alkali-induced growth inhibition. It restored antioxidant indices, reduced the accumulation of malondialdehyde (MDA), H₂O₂, and O₂⁻, increased leaf area, and elevated chlorophyll content. Combined transcriptomic and metabolomic analyses identified 2896 and 3530 differentially expressed genes (DEGs) in HN95 and HF50, respectively, under ICe6 vs SA treatment. These DEGs were mainly enriched in photosynthesis and chlorophyll metabolism pathways such as GO:0009765 (photosynthesis, light harvesting). Differentially accumulated metabolites were mainly enriched in the isoflavonoid biosynthesis pathway (flavonoids enhance antioxidant capacity) and the amino acid biosynthesis pathway (determines chlorophyll precursor synthesis efficiency). These results indicate that ICe6 primarily regulates the expression of chlorophyll metabolism-related genes, light energy capture, and chlorophyll biosynthesis, thereby increasing chlorophyll content, promoting carbohydrate accumulation, and ultimately improving soybean yield under saline-alkali stress (HN95: +5.74%; HF50: +5.83%).