To make full use of tuna by-products to prepare high-value products, skipjack tuna (Katsuwonus pelamis) milt was degreased, pretreated with microwave and separately hydrolyzed using trypsin, Neutrase, papain, and pepsin. Neutrase hydrolysate with the highest degree of hydrolysis (29.54 ± 1.19 %) and antioxidant activities were separated by ultrafiltration and a series of chromatographic methods, and thirteen antioxidant oligopeptides were prepared and identified as GHHAAA, PHPR, AKHQ, GRVPRV, ADMYW, VDDDD, SVTEV, VKIYI, VRDQY, IRDDY, YREY, AQRPR, and SMDV with molecular weights of 562.6, 505.6, 482.7, 654.8, 685.1, 578.0, 534.2, 634.6, 679.2, 681.2, 630.0, 626.4, and 450.0 Da, respectively. Moreover, GHHAAA, PHPR, SVTEV, VRDQY, and SMDV showed the highest Ferric-reducing power and radical scavenging activity on DPPH (EC50 values of 1.09 ± 0.08, 1.19 ± 0.07, 0.89 ± 0.08, 0.88 ± 0.11, and 1.24 ± 0.09 mg/mL, respectively) and ABTS (EC50 values of 1.12 ± 0.06, 1.14 ± 0.11, 1.02 ± 0.07, 1.04 ± 0.12, and 1.16 ± 0.07 mg/mL, respectively). In addition, GHHAAA, PHPR, SVTEV, VRDQY, and SMDV presented significant protective function on H2O2 oxidative damaged HUVECs by increasing the HUVECs viability and antioxidant enzyme activity, and lower the contents of ROS and MDA. This study suggested that GHHAAA, PHPR, SVTEV, VRDQY, and SMDV could be natural antioxidant ingredients used in pharmaceutical and functional products.