Hydrolysates of soy protein isolate-maltodextrin (SPI-Md) conjugate were used as wall material to prepare fish oil microcapsules by freeze-drying method. Effects of the protein structural modifications on the physicochemical properties of the emulsion and the oxidative stability of the microcapsules were characterized. Compared with emulsions of SPI-Md conjugates or soy protein isolate/maltodextrin (SPI/Md) mixture, lower droplet size (212.5-329.3nm) and polydispersity index (PDI) (0.091-0.193) were obtained in the fish oil emulsions prepared by SPI-Md conjugate hydrolysates. The improved amphiphilic property of SPI-Md conjugate hydrolysates was supported by the results of surface and interfacial tension, and further confirmed by the improved emulsion stability during the storage period. Although the microencapsulation efficiency (MEE) of SPI-Md conjugate hydrolysates slightly decreased from 97.84% to 91.47% with the increasing degree of hydrolysis (DH), their oxidative stabilities (peroxide value and headspace propanal) were apparently improved compared with native SPI/Md mixture or SPI-Md conjugates system. Moreover, favorable thermal stability as well as a porous and uniform surface structure of the microcapsules coated by SPI-Md conjugate hydrolysates (DH 2.9%) was observed via the thermal analysis and scanning electron microscope (SEM) micrographs, respectively.