Cobalt nanoparticles (CoNPs) represent an environmental risk factor for Alzheimer’s disease (AD), involving disrupted calcium homeostasis and m6A modification. Using Caenorhabditis elegans, human neuroblastoma SH-SY5Y cells, and C57B/L mice, this study demonstrates that CoNPs upregulate the m6A demethylase ALKBH5, reducing global neuronal m6A levels and specifically on MICU1 mRNA (binding confirmed by molecular docking and RNA-pulldown), leading to increased MICU1 protein. This MICU1 upregulation drives mitochondrial calcium overload, fragmentation, and respiratory dysfunction. On the other hand, we have observed that CoNPs triggered a 2.7-fold increase in the formation of vesicles derived from the inner mitochondrial membrane (VDIM) compared with the control. VDIM enables inner membrane-specific degradation of damaged components—a precision repair mechanism activated by MICU1-mediated injury. Notably, ALKBH5 knockdown exacerbated CoNPs-induced calcium overload and mitochondrial damage, while MICU1 overexpression rescued these defects; VDIM levels correlated directly with MICU1 expression. Taken together, this work is the first to elucidate an epigenetic (m6A/ALKBH5) axis governing mitochondrial calcium homeostasis (via MICU1) and downstream precision repair (VDIM). It reveals a novel CoNPs neurotoxicity pathway relevant to AD pathogenesis, identifying ALKBH5/MICU1 as therapeutic targets and pioneering epitranscriptomic regulation in organelle-specific quality control.