Background <p>Ovarian cancer remains one of the deadliest cancers in women, characterized by poor prognosis and limited therapeutic options. The role of specific molecular factors, particularly in the context of tissue stem cells, DNA methylation, and metabolic reprogramming, is not fully understood. A-kinase anchoring protein 12 (<i>AKAP12</i>), a gene implicated in various cancers, has yet to be thoroughly explored in ovarian cancer. This study aims to investigate <i>AKAP12</i>’s involvement in ovarian cancer prognosis, focusing on its expression profile, regulation via DNA methylation, and its downstream metabolic effects.</p> Methods <p>We performed a comprehensive multi-omics analysis integrating single-cell RNA sequencing, Mendelian randomization (MR), and DNA methylation profiling, immune infiltration analysis and pathway enrichment analysis. First, we identified <i>AKAP12</i> as a central prognostic gene in ovarian cancer by intersecting TCGA’s prognostic gene list with ovarian cancer stem cell marker genes. We examined <i>AKAP12</i> expression in single-cell RNA sequencing data and analyzed the relationship between DNA methylation and <i>AKAP12</i> expression. A multi-cohort analysis including datasets from TCGA and two independent GEO datasets (GSE26712 and GSE17260) further assessed <i>AKAP12</i>’s association in immune cell infiltration. Further mediated MR analysis was applied to determine the role of metabolic factors that mediate the role of <i>AKAP12</i> on ovarian cancer. In silico virtual knockout of <i>AKAP12</i> was performed on single-cell data to model its functional impact.</p> Results <p><i>AKAP12</i> was predominantly expressed in ovarian cancer stem cells and a subset of epithelial cells, contrasting with its expression in normal ovarian stromal cells. DNA methylation at loci cg10270306 and cg22942200 causally regulated <i>AKAP12</i> expression and patient survival. The ADP/FAD (adenosine diphosphate/flavin adenine dinucleotide) ratio was identified as a key protective metabolic mediator, explaining 10.09% of <i>AKAP12</i>’s effect on prognosis. <i>AKAP12</i>-high tumors exhibited altered redox metabolism and ECM remodeling pathways. Critically, virtual knockout of <i>AKAP12</i> causally disrupted the transcriptional network governing ECM composition and cell-ECM interactions.</p> Conclusion <p>Our study establishes <i>AKAP12</i> as an upstream regulator of ovarian cancer progression, modulated by DNA methylation and exerting its effect through metabolic reprogramming (via the ADP/FAD ratio) and ECM remodeling. These findings provide new insights into the molecular mechanisms driving ovarian cancer and suggest therapeutic strategies targeting the <i>AKAP12</i> regulatory network.</p>