This study aimed to investigate the structure-activity relationship of the pine nut antioxidant peptide WYPGK and its derivative peptides, and to evaluate the protective effect of the latter on oxidative damage to mitochondrial structure and function in PC12 cells. Molecular docking revealed the derivative peptides WYFGK and WYSGK to have higher affinity to the active region of sirtuin 3 (SIRT3) (−6.08 kcal/mol and −5.87 kcal/mol, respectively), hence indicating that they are promising SIRT3 inducers and antioxidant factors. The derivative peptide WYSGK presented the highest ORAC value (5457.70 µmol TE/g), ABTS scavenging activity (70.05%), and Fe2+-chelating activity (81.70%), followed by WYPGK and WYFGK. Circular dichroism and nuclear magnetic resonance data suggested that the presence of 3-Ser in WYSGK increased its β-sheet content, and that the active hydrogen atoms produced chemical shifts. In H2O2-induced PC12 cells, WYSGK substantially reduced ROS and MDA levels, and increased ATP levels. Transmission electron microscopy and Seahorse Analyze assay proved the peptide WYSGK to significantly alleviate mitochondrial damage and respiratory dysfunction (p < 0.05), thereby implying that a study of structure-activity relationships of the peptides can possibly be an effective approach for the development of functional factors.