Incorporation of fish oil containing ω-3 polyunsaturated fatty acids (PUFAs) into functional foods remains challenging. In this study, caseinate and glycoconjugates (CD6, CD40, CD70, CD100) of caseinate to dextrans of different molecular weights (D6, D40, D70, D100 kDa) were used to stabilize fish oil emulsions, and the impact on physicochemical stability and gastrointestinal fate was investigated. The glycoconjugate of CD6 exhibited significantly higher conjugation efficiency, lower surface hydrophobicity (H0), and lower surface activity than other glycoconjugates. The glycoconjugate of CD70 displayed the best emulsifying activity and emulsion stability. Except CD6 stabilized emulsions, all other emulsions showed fine storage stability over 14 d at 22 ± 1 °C. The glycoconjugate stabilized emulsions exhibited significantly lower peroxide value (PV) (P < 0.05) than that of the caseinate stabilized one. During in vitro gastrointestinal tract digestion, the glycation of caseinate with dextrans changed the ζ-potential, average particle size (D 32), and particle size distribution of the emulsions, which influenced flocculation and coalescence of droplets, as demonstrated by confocal microscopy. Caseinate after glycation with dextrans significantly retarded the release of free fatty acids from emulsions (P < 0.05) during in vitro lipolysis. These results suggested that the dextrans attached to caseinate by glycation played a vital role in physicochemical stability and gastrointestinal fate of emulsions, mainly by its steric hindrance to effectively prevent flocculation and coalescence of droplets.