The purpose of present study was to separate novel antioxidant peptides from duck breast protein hydrolysates and characterize their primary sequence, secondary and tertiary structure using Nano-LC-ESI-LTQ-Orbitrap MS/MS, NICOLET IS10 FT-IR and PEPstr server, respectively. Results indicated that peptide fraction P1 via gel filtration chromatography displayed high DPPH radical quenching effect and reducing power. Fraction P1 was further purified chromatographically and sequenced as eleven novel antioxidant peptides, in which AGPSIVH possessed the best DPPH inhibition, and LLCVAV exhibited active reducing power, whereas FLLPH and LLCVAV were effective ABTS•+ scavengers. IR study and PEPstr server prediction suggested that spatial structure could play an influential part in antioxidant capacity. Importantly, these peptides were predicted as non-toxic oxidative stress inhibitors, allowing their applications in functional foods.