The invention discloses a soybean fermentation metabolin. Components of the metabolin comprise amino acid and a derivative thereof, amine, sugar phosphate, nucleoside, a nucleoside derivative, organicacid and fatty acid. In addition, the invention further discloses a preparation method and application of the soybean fermentation metabolin. The soybean fermentation metabolin has the remarkable effects of improving diversity and quality of skin bacterial flora, skin water content and skin acid mantle, and is capable of avoiding loss of skin beneficial substances, maintaining balance of the skinbacterial flora, reinforcing nonspecific immune response, preventing skin infection and inflammation, and preventing skin related diseases, such as pruritus, acne, scurf, rubeosis and drying.