Epigenetic modifications include DNA methylation, RNA methylation, histone methylation, histone acetylation, and noncoding RNA. This article elucidates the molecular mechanisms by which histone modifications regulate key proteins associated with neurological disorders, focusing on how the dynamic balance between histone acetyltransferase (HAT) and histone deacetylase (HDAC) serves as an epigenetic regulatory hub, influencing disease progression through acetylation coding. It also summarizes how fluctuations in acetyl coenzyme A/nicotinamide adenine dinucleotide levels regulate cell death networks via HAT and the silence information regulator family, as well as multi-target therapeutic strategies combining HDAC inhibitors, iron chelators, and receptor-interacting protein kinase 1 inhibitors to achieve precise neuroprotection.