A human milk fat (HMF) analogue synthesis from tripalmitin, stearidonic acid (SDA) soybean oil, and docosahexaenoic acid (DHA) was scaled up by interesterification catalyzed by Novozym 435 and acidolysis by Lipozyme TL IM, and then purified by short-path distillation (SPD). This structured lipid (SL) contained 5.4 mol% DHA and 8.0 mol% SDA, with 57.0 mol% palmitic acid esterified at sn-2 position. Although tocopheryl and tocotrienyl fatty acid esters were formed during interesterification and acidolysis, >50% of vitamin E isomers were lost into distillates (wastes) during SPD, which contributed mostly to the rapid oxidative deterioration of SLs in the recent and past studies. Response surface methodology was applied to investigate the effects of lecithin, monoacylglycerol, locust bean gum (LBG), and carrageenan on the physical and oxidative properties of SL-based infant formula (IF) emulsion. Particle size, optical stability, viscosity, relative content of DHA and SDA, and total oxidation value were assessed during 28-day storage. In addition, the effect of permitted antioxidants (added at 0.005 and 0.02% of oil, respectively), including -tocopherol, -carotene, ascorbyl palmitate, ascorbic acid, citric acid, and their combinations, on the lipid oxidation was evaluated under an accelerated storage. The peroxide value, anisidine value, and hexanal concentration of emulsion samples were measured. It was found that the optimal conditions to achieve the highest physical and oxidative stability of SL-based IF emulsion were 0.2 g/100 mL lecithin, 0.4 g/100 mL monoacylglycerol, 0.045 g/100 mL LBG, 0.015 g/100 mL carrageenan, and 0.005% ascorbyl palmitate. On the basis of measurement of peroxide and anisidine values over a 28-day period, annatto TRF was found to be a more effective antioxidant than palm TRF and -tocopherol in inhibiting lipid oxidation in menhaden fish oil and SL-based IF emulsion at 0.02% and 0.05%. Addition of -tocopherol (0-75%) did not interfere with the antioxidant activity of tocopherol-free annatto TRF in the foods tested. Overall, this study has important implications for the successful incorporation of SL into IF products for better infant nutrition and health.