Background <p>Migraine is a debilitating neurological disorder. Emerging evidence suggests that metabolic dysregulation and immune dysfunction contribute to migraine pathogenesis while the molecular mechanisms linking these processes remain unclear. Lactylation may serve as a crucial integrator of metabolic and immune signals in migraine.</p> Methods <p>We performed a comprehensive multi-omics Mendelian randomization study integrating DNA methylation, gene expression, and protein abundance data with genome-wide association studies on migraine. Summary-data-based Mendelian randomization, Bayesian colocalization, and two-sample MR analyses were conducted to identify lactylation-related genes causally associated with migraine. We further explored immune cell mediation using genetic data from 731 immune phenotypes and validated findings through single-cell RNA sequencing of peripheral blood mononuclear cells from migraine patients and controls.</p> Results <p>EP300, SIRT1, and SLC16A1 were identified as key regulators of migraine susceptibility across methylation, expression, and protein levels. EP300 and SLC16A1 were associated with increased migraine risk, while SIRT1 conferred a protective effect. Mediation analyses revealed that genetic effects of these genes were partially transmitted through specific immune cell subsets, particularly B cells and natural killer T cells. Single-cell transcriptomic profiling further demonstrated EP300 upregulation in B cells and T cells of migraine patients. These findings support a novel “lactylation–immune mediation–migraine axis” linking metabolic and immune dysregulation to migraine pathogenesis.</p> Conclusion <p>This integrative multi-omics analysis uncovers lactylation-related genes as causal drivers of migraine through immunometabolic pathways. Targeting lactylation-regulated metabolic and immune mechanisms may offer novel precision therapeutic strategies for migraine, particularly in patients with inflammatory or metabolic endophenotypes.</p>