Exploring natural antiphotoaging agents is highly desirable. Bifidobacterium longum subsp. iuvenis (Bl. iuvenis) is a newly identified subspecies found in the intestines of infants, and its functions, components and metabolites have not yet been fully elucidated. Here, we demonstrated that Bl. iuvenis YSG is highly efficient in reducing UVB-induced melanin production in melanocytes. Through differential metabolomics analysis, we identified the metabolites 5-hydroxyindole-2-carboxylic acid and aconitic acid as Bl. iuvenis YSG-specific anti-melanogenic substances. Bl. iuvenis YSG potently inhibited melanogenesis by downregulating melanogenic enzymes and directly acting on tyrosinase active sites. Furthermore, B. longum inhibited ROS generation in keratinocytes through its metabolite glycolic acid, increasing the levels of elastin, collagen III and collagen XVII in fibroblasts. We demonstrated that Bl. iuvenis YSG-derived fermentation components not only reduced the number of sunburn cells in UV-irradiated reconstituted human epidermis but also ameliorated ECM damage and epidermal atrophy in ex vivo human epidermis. Our results suggest that mixed metabolites derived from Bl. iuvenis synergistically contribute to antiphotoaging effects, specifically through the production of specific organic acids. These findings revealed that Bl. iuvenis is a novel potential protective agent for photoaging and provided an in-depth study of the underlying mechanism.