Oxidative rancidity is a major issue limiting the utilization of flaxseed oil (FSO). Peptides possess an antioxidant effect; however, the flax cyclic peptide, a unique ingredient in FSO, has an obscure influence on the oxidation of FSO. Therefore, this study is aimed to investigate the effects of [1-9-NαC]-linusorb B3 (CLA) on the accelerated oxidation of FSO and the underlying mechanism. We found that CLA increased the antioxidant stability of refined flaxseed oil (RFO), indicated by the improved parameters involved in the oxidation after the addition of CLA. After accelerated oxidation, the acid value (AV) of the RFO was increased by 24.14 times, whereas that of the RFO with CLA (CLA-RFO) increased only by 7.21 times. Similarly, the peroxide value (POV) and P-anisidine value (P-AV) of CLA-RFO were significantly decreased. Besides, CLA influenced metal ions-induced oxidation. In the Cu 2+ group, the addition of CLA reduced the AV by 18% and the POV by 20%. The results of the molecular docking analysis and fluorescence quenching showed that the metal ions and propionaldehyde interacted with the cavity of CLA, and propionaldehyde had the most stable binding configuration with CLA, indicating that CLA may slow down the oxidation of FSO by chelating the metal ions and the intermediate oxidative products.