We identified novel antioxidant peptides from Pacific saury (Cololabis saira). Enzymatic hydrolysates were isolated, purified, and identified by ultrafiltration, gel chromatography, reverse phase high-performance liquid chromatography (RP-HPLC), and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS). Twenty putative peptides were identified from five components of HPLC, among which sixteen peptides were predicted to have good water solubility and non-toxicity by online tools. Fifteen peptides were successfully docked with myeloperoxidase, and we observed that Arg31, Arg323, and Lys505 played a key role in the antioxidant mechanism, with van der Waals forces and conventional hydrogen bonds as important interaction forces. Six identified peptides with lower CDOCKER energy values were synthesized to verify the antioxidant activity, and the results showed that the synthetic peptide QQAAGDKIMK displayed the strongest 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging rate (31.05 ± 0.27%) and reducing power (0.29 ± 0.01). The synthetic peptide KDEPDQASSK at a concentration of 300 μg mL-1 exhibited the strongest protective effects on H2O2-induced oxidative damage of HEK-293 cells, with cell viability and ROS level of 0.38 ± 0.03 and 0.08 ± 0.01, respectively.