Neurons are highly susceptible to mitochondrial dysfunction due to their post-mitotic nature and high metabolic demands. Mitophagy, an important mitochondrial quality control mechanism, selectively captures and delivers damaged mitochondria to lysosomes for degradation. The protein kinase PINK1 and the E3 ubiquitin ligase Parkin are key initiators of damage-induced mitophagy, and mutations in these proteins are associated with autosomal recessive early-onset Parkinson’s disease (PD). Oxidative stress, resulting from dysfunctional mitochondria, is a core contributor to neurodegeneration in PD. While mitophagy is essential for maintaining mitochondrial quality, the mechanisms by which mitophagy is regulated in neurons, particularly under mild oxidative stress, remain poorly understood. Furthermore, axonal degeneration is thought to be a primary event in PD pathogenesis, yet the role of mitophagy in this context is not fully elucidated. In this study, we address three fundamental questions: 1) How are damaged mitochondria recognised and eliminated by PINK1/Parkin-mediated mitophagy in axons? 2) What are the consequences of a breakdown in PINK1/Parkin-mediated mitophagy? 3) Can the effects of PINK1/Parkin mitophagy defects be rescued by promoting an alternative mitophagy pathway, such as NIX/BNIP3-dependent mitophagy? We employed several advanced imaging techniques, including 3D correlative light and volume scanning electron microscopy, and a 3D reconstruction method developed in our lab, termed AIVE (Artificial Intelligence-directed Voxel Extraction). Our findings show that axonal PINK1/Parkin-mediated mitophagosome formation primarily occurs at presynapses. In neurons with defective PINK1/Parkin mitophagy, we observed local accumulation of damaged mitochondria, cytochrome c leakage, and cleaved caspase-3 in presynapses, and live cell imaging of axon degeneration, suggesting increased susceptibility to oxidative stress and initiating axonal degeneration in presynapses. This study uncovers a neurodegenerative mechanism linking axonal vulnerabilities observed in PD with mitophagy defects. We also demonstrate that pharmacological rescue of axonal degeneration can be achieved by synthetic upregulation of receptor-mediated mitophagy using the clinically approved compound Roxadustat, revealing a potential therapeutic avenue for PD. Collectively, these findings enhance our understanding of how mitophagy machinery maintains neuronal health and guide the development of mitophagy modulators as potential PD therapeutics.