Organic selenium has been widely explored as an important source of selenium (Se) supplement due to its low toxicity and easy absorption. In the present study, a new type of organic selenium was fabricated by chelating Se with soybean protein isolate peptides (SPIPs), and its physio-chemical properties, structural characteristics, and antioxidant activities were investigated. Results indicated that the structure of the SPIP molecule was folded and aggregated during the chelation process. SPIP-Se exhibited stronger hydroxyl radical scavenging activity and reducing power than SPIP in vitro. In addition, SPIP-Se could repair the H2O2-induced oxidative damage of Caco-2 cells by enhancing the activities of antioxidant enzymes. The in vivo assay showed that SPIP-Se showed much less toxicity than inorganic Se supplements, and exhibited a more positive effect on the activities of key enzymes including superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and aspartate aminotransferase (AST). These findings suggest that SPIP-Se could be developed as an effective dietary Se supplement in the food or pharmaceutical field in the future.