Abstract: Neurodegenerative diseases (NDs) are chronic disorders marked by progressive neuronal loss, with pathogenesis involving abnormal protein aggregation, oxidative stress, mitochondrial dysfunction, and other contributing factors. As a core mechanism regulating mitochondrial quality control and cellular homeostasis, mitophagy has gained increasing attention as a therapeutic target in NDs. Food-derived bioactive peptides have attracted interest due to their high safety and low toxicity, demonstrating considerable potential for the nutritional intervention of NDs. This review systematically outlines the molecular mechanisms of mitophagy and its dysregulation in neurodegenerative conditions, with a focus on how specific dietary peptides—including corn, rice, walnut, and marine collagen peptides—modulate mitophagy and restore mitochondrial function via pathways such as PINK1/Parkin, AMPK/mTOR, and Bnip3/Nix. We also summarize evidence regarding their efficacy in reducing neuronal apoptosis and improving cognitive performance in animal models. This work provides a theoretical foundation for the use of food-derived peptides in neuroprotective nutritional strategies and offers insights for developing functional foods and early dietary interventions against NDs.