This study investigated the impact of hydrogen (H2) treatment under ultraviolet B (UV–B) irradiation on the growth status, antioxidant system, metabolite changes, and isoflavone content and composition of germinated soybeans. The results showed that compared with UV-B alone, H2 promoted the growth of germinated soybeans by regulating the content of metabolites (nucleotides, fats, amino acids, hormones, and neurotransmitters) and related metabolic pathways. H2 resists UV-B stress by binding directly to reactive oxygen species or mediating the antioxidant system. Increased activity and gene expression of phenylalanine ammonia-lyase, cinnamic acid-4-hydroxylase, and 4-coumaric acid coenzyme A ligase promoted isoflavone enrichment and promoting the conversion of glycosides to aglycones by reducing the activity and gene expression of isoflavone 7-O-glucosyltransferase and isoflavone 7-O-glucoside-6″-O-malonyltransferase. These results explain to some extent the possible reasons for the H2 treatment to alleviate UV-B stress, promote the growth of germinated soybeans, and enrich isoflavones (especially aglycones).