The invention belongs to the field of microbial fermentation, and especially relates to a fermentation metabolite having an effect of protecting skins, and a preparation method and applications thereof. The product is prepared by taking lactobacillus plantarum, lactobacillus casei, lactobacillus lactentis, bifidobacterium animalis and lactobacillus rhamnosus as fermentation strains and taking sucrose, seaweed meal, soybean meal and milk powder as fermentation raw materials through mixing and fermentation. The product contains specific fermentation metabolites, such as malonylgenistin, genistein, hyaluronic acid, irone, Preaustinoid A and daidzein, which are helpful for the enhancement of a skin protection effect; and tartaric acid, malic acid, succinic acid, salicylic acid, vanillic acid, phenylpropionic acid and other organic acid generated by fermentation can control pathogenic bacteria and spoilage microbial flora, so that skin flora balance can be maintained, and a natural antiseptic effect can be achieved. Efficacy tests show that the product has the efficacy of removing wrinkles, increasing skin elasticity, resisting inflammation and repairing skin barriers, and is significant in effect.