Precision nutrition and nutrimetabolomics are emerging omics technology applications in public health. In this context, the infant formula (IF) is a manufactured foodstuff that aims to match the composition of human milk (HM), especially the lipid profile. The IF manufacturers have achieved relative success in matching the predominant fatty acid (FAs) profiles, but the stereospecific structures of the triacylglycerides in HM require deeper analyses with system sciences. We employed NMR-based metabolomics to compare the lipid profiles of 12 commercial IF samples and 10 HM samples. Additionally, vegetables, fish, and microalgae oil as raw materials in IFs were also investigated to understand the lipid profile of IFs. We found that IF has significantly less saturated fatty acids (SFA), higher unsaturated FAs, and similar polyunsaturated fatty acid (PUFA) content, compared with HM. However, the main difference was the stereospecific distribution of FAs: HM samples were associated with a high content of SFAs in the sn-2 position (26.03% -2.93%) and PUFAs in the sn-1,3 position (15.35% -3.94%). The IF had the opposite distribution, with SFAs esterified mainly in the sn-1,3 position (33.07 -4.93%) and PUFAs in the sn-2 position (9.57% -7.05%). Consequently, the hydrolysis of HM results in SFA mainly as sn-2-monoacylglycerides, which are well absorbed. In contrast, the hydrolysis of the IF provided SFA, mainly as free FAs, which tend to bind calcium and form insoluble calcium soaps in the intestine. Taken together, these observations can inform optimal design of infant formulas with a view to precision nutrition.