In this study, the in vitro digestion model was used for investigating the impacts of the application of Mono-, Di-glyceride (MDG) and phospholipid (PL) in the infant formula model emulsions on the bioaccessibility of lipophilic nutrients (vitamin D, carotenoids) contained in the formula. The addition of MDG/PL were found to significantly facilitate the micellization of lipophilic nutrients contained in the infant formula-based emulsion system at the simulated small intestine stage and led the digestion behavior more similar to human breast milk. The higher micellization rate resulted in higher absorption efficiency and higher bioavailability of liphophilic nutrients in the infant formula. Furthermore, the structures of MDG also impacted the bioaccessibility of lipophilic nutrients contained in the formula and the results indicated that the presence of oleic acid structure in the MDG molecules showed the higher effectiveness on enhancing the bioaccessibility of lipophilic nutrients.