Selenium-biofortified crops are a quality functional food resource because of their anti-tumor and anti-cancer properties. In the present study, the conjugates of selenium-biofortified soybean protein and polyphenols were prepared and evaluated by alkali-induced synthesis and in vitro antioxidant tests. Moreover, the antioxidant mechanisms of protecting mice skin damaged by UV-B were studied. The results showed that the antioxidant activity of the conjugate between 7S globulin from selenium-enriched soybean (Se-7S) and EGCG (Se-7S-EGCG) was significantly higher (P < 0.05) than that of Se-7S-GA. Structural characterizations implied that the polymerization of polyphenols with amino acid residues occurred. Se-7S-EGCG inhibited the apoptosis of epidermal cells induced by UV-B. The overexpression of phosphorylated proteins in the MAPK signaling pathway, the activation of related inflammatory factors, and the boost in the MMPs were reversed by Se-7S-EGCG. Overall, this research provides a theoretical and experimental basis for the application of protein and polyphenol conjugates in food and medicine fields.