Mitochondrial dysfunction is a core pathogenic mechanism underlying a broad spectrum of neurodegenerative disorders, from Alzheimer's and Parkinson's diseases to inherited optic neuropathies and mitochondrial ataxias. This review provides a comprehensive analysis of how defects in mitochondrial and nuclear DNA converge to disrupt oxidative phosphorylation, mitochondrial dynamics, calcium homeostasis, and quality control pathways, leading to energy depletion, oxidative stress, and neuronal degeneration across multiple disease contexts. Building on this mechanistic foundation, we examine how these shared pathogenic principles manifest distinctly in major neurodegenerative diseases, while also discussing representative mitochondrial optic neuropathies as tractable disease models that have yielded critical mechanistic and therapeutic insights. We further review recent advances in diagnostic technologies that enhance our ability to detect and stratify mitochondrial pathologies for therapeutic intervention. On the therapeutic front, we provide a comprehensive evaluation of the rapidly evolving landscape, analyzing strategies ranging from metabolic modulators and antioxidants to pioneering gene-targeted therapies, organelle replacement approaches, and emerging epitranscriptomic interventions. Finally, we identify persistent challenges in clinical translation and outline pivotal future directions essential for developing effective, mechanism-informed combination therapies against mitochondrial dysfunction in neurodegeneration.