Lipids are essential sources of carbon and energy during flaxseed germination; however, the dynamic changes in key lipid metabolites, pathways, and their locations remain unclear. This study revealed that oil bodies migrated from well-distributed locations to the cell wall between 0-2 d, with cell contours gradually blurring during 2-3 d, initiating the germination process. Subsequently, the order of oil body migration was leaf > stem > root during 4-7 d. This study established lipid metabolite pathway networks to elucidate the underlying mechanisms of the interconversion of active lipid metabolites. Phosphatidyl methyl ethanolamines (PMEs) (18:2/23:0), (24:0/18:2), and (24:0/18:3) were utilized as energy substrates through alpha-linolenic acid metabolism, autophagy, and glycosylphosphatidylinositol (GPI)-anchor biosynthesis pathways during 2-3 d. The production of phosphatidic acid (PA) (18:1/18:1) exceeded its consumption in glycerolipid metabolism, glycerophospholipid metabolism, and the phosphatidylinositol signaling system, resulting in the consumption of phosphatidylethanolamine (PE) ((16:0/16:0), (24:0/24:0)) during 3-4 d. The active metabolite phosphatidylcholine (PC) (18:1/18:1) converted to PA and PE in leaves, stems, and roots and to triacylglycerol (TG) in stems and roots during 4-6 d. Oil bodies existed in leaves (ceramide (Cer), TG) and roots (TG) during 6-7 d. These findings elucidate the metabolic processes underlying seedling development, paving the way for crop improvement.