Prior studies have indicated that the neuroprotective effects of dexmedetomidine (DEX) in cerebral ischemia, yet its mechanisms remain elusive. Using multi-omics approaches (RNA-seq, metabolomics, and single-cell RNA-seq), we discovered that DEX pretreatment significantly reduced cerebral infarct volume and improved neurological function in middle cerebral artery occlusion (MCAO) mice compared to PBS controls. Single-cell analysis revealed that DEX preserved microglial phagocytic function via metabolic regulation, leading to reduced microglial apoptosis and attenuated immune dysregulation-including decreased chemotactic neutrophils, B cells, and antigen-presenting fibroblasts. These cellular changes were corroborated by transcriptomic and metabolic profiles showing suppressed apoptosis and inflammation. Mechanistically, we identified HK2 (hexokinase 2) as a key regulator of microglial homeostasis, with its expression correlating with microglial migration, proliferation, and inflammation, findings validated in oxygen-glucose deprivation models. Collectively, our results demonstrate that DEX protects against cerebral ischemia-reperfusion injury by maintaining immune microenvironment homeostasis through microglial metabolic reprogramming mediated by HK2. This multi-omics study provides mechanistic insights supporting DEX's translational potential in ischemic stroke therapy.