Red light, an important light environmental signal regulating plant stem growth and development. Using proteomics and metabolomics approaches, this study investigated differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) in soybean hypocotyls between soybean plants under darkness and red-light conditions, which elucidated the pathways underlying the regulatory effects of red light on soybean hypocotyl growth. The results revealed that red light can inhibit hypocotyl elongation and increase the hypocotyl diameter of soybean. Red light inhibited hypocotyl elongation mainly by enhancing the firmness of the cell wall. On the one hand, red light promoted the expression of enzymes related to the conversion of serine and threonine to glycine, decreased the level of intracellular reactive oxygen species, and then reduced the degradation of cell wall polysaccharides. On the other hand, by enhancing the expression of enzymes related to the lignin monomer synthetic pathway, red light promoted the synthesis of lignin monomers to strengthen the cell wall. Meanwhile, red light promoted hypocotyl thickening mainly by upregulating the expression of aminocyclopropanecarboxylate oxidase, promoting the accumulation of ethylene precursors (S-Methyl-5’-thioadenosine and 1-aminocyclopropane-1-carboxylic acid), and accelerating ethylene synthesis. This study provided a theoretical basis for using light to regulate soybean stem growth.