This study presents a comprehensive lipidome map of the human brain, comprising 75 anatomically and functionally distinct regions. The lipidome composition varies significantly among these regions, affecting 93% of the analyzed lipids. These differences are influenced by structural characteristics such as myelin content and cell type composition, as well as functional traits like functional connectivity and information processing hierarchy. The study combines lipid composition data with mRNA expression data to enhance the understanding of functional connectivity. Biochemically, lipids linked to structural and functional brain features exhibit distinct lipid class distribution, unsaturation extent, and prevalence of omega-3 and omega-6 fatty acid residues. The findings are validated through parallel analysis of three adult macaque brains and targeted analysis of 216 lipids. The study bridges the gap between brain structural and functional architecture studies and microscale molecular organization analyses, providing insights into the role of lipids in brain organization and function.This study presents a comprehensive lipidome map of the human brain, comprising 75 anatomically and functionally distinct regions. The lipidome composition varies significantly among these regions, affecting 93% of the analyzed lipids. These differences are influenced by structural characteristics such as myelin content and cell type composition, as well as functional traits like functional connectivity and information processing hierarchy. The study combines lipid composition data with mRNA expression data to enhance the understanding of functional connectivity. Biochemically, lipids linked to structural and functional brain features exhibit distinct lipid class distribution, unsaturation extent, and prevalence of omega-3 and omega-6 fatty acid residues. The findings are validated through parallel analysis of three adult macaque brains and targeted analysis of 216 lipids. The study bridges the gap between brain structural and functional architecture studies and microscale molecular organization analyses, providing insights into the role of lipids in brain organization and function.