This study investigated the effects of selenium biotransformation on the composition, structure, functional properties, and in vitro antioxidant activity of goat milk casein, as well as its gastrointestinal digestibility properties and selenium bioavailability. The results showed that the total selenium content in selenium-enriched goat milk casein was 498.21 μg/100 g, with organic selenium comprising up to 99.92%. Selenium transformation did not induce significant changes in the major composition of goat milk casein, and although the secondary structure of the protein and certain functional properties exhibited minor alterations, the overall stability was maintained. The antioxidant activity of seleniumenriched goat milk casein was positively correlated with protein concentration and selenium content. Upon reaching a specific threshold of protein concentration, its antioxidant capacity was significantly superior to that of ordinary goat milk casein. In vitro simulated gastrointestinal digestion showed that selenium transformation did not significantly influence the digestibility of goat milk casein, with its selenium bioavailability reaching as high as 90.75%. Moreover, the antioxidant activity of the digestion products was further enhanced and significantly better than that of the non-selenium-enriched group. Comprehensive analysis revealed that selenium-enriched goat milk casein possessed a high organic selenium content, good protein structure and functional stability, superior antioxidant activity, favorable digestion characteristics, and high selenium bioavailability, thereby positioning it as a promising high-value-added functional selenium-enriched milk protein product.