In view of our rapid growing demands on vegetable oil, enhancing fatty acid synthesis in maize (Zea mays) represents tremendous nutritional and economic benefits. In corn kernels, the endosperm and the embryo are the main site for synthesis and accumulation of starch and oil, respectively. So far, breeding efforts to achieve elevated oil content in maize resulted in smaller endosperm and therefore lower yield. We hypothesize that the key to increasing oil content in maize kernels without affecting the yield lies on directly changing their carbon metabolism. To test our hypothesis, we compared the intracellular metabolite levels in maize embryos from two different maize lines, Alex synthetic (Alex) and LH59, which accumulate 48 and 34% of oil, respectively. The comparative metabolomics highlighted the metabolites and pathways that were active in maize embryos and important for oil production. The contribution of each pathway to fatty acid synthesis in terms of carbon, reductant and energy provision was assessed by measuring the carbon flow through the metabolic network (13C‐Metabolic Flux Analysis) in developing Alex and LH59 embryos to build maps of carbon flow through central metabolism. Our approach combined mathematical modeling with biochemical quantification to identify metabolic bottlenecks in fatty acid synthesis in maize embryos. Transgenic maize plants that we generated to overexpress a lead gene increased embryo fatty acid content by 35% without affecting the size of the kernel. This study hence describes the combination of innovative tools that will pave the way for controlling seed composition in important food crops.