To elucidate the roles of interfacial protein microstructure in regulating techno-functional attributes of complex microgel, this work explored the effects of transglutaminase cross-linking alone or in combination with ultrasonication on conformation and functional properties of whey protein isolate-chitooligosaccharide microgel dispersion (WPI–COS). It was found that transglutaminase-crosslinked WPI-COS microgels presented improved interfacial properties when a moderate unfolding process was induced by sonication, validating the existence of optimum flexibility of complex Pickering particles during unfolding/refolding of interfacial proteins. Particularly, TG induced excessive crosslinking of WPI-COS to form aggregates, causing a lower surface hydrophobicity. In contrast, ultrasound was inclined to increase the surface hydrophobicity for TG-catalyzed and uncatalyzed samples, suggesting differential unfolding degrees of WPI induced by transglutaminase and ultrasonication. Correspondingly, interfacial properties of ultrasonicated WPI-COS complexes, as revealed by percentage of adsorbed protein, interfacial tension and three-phase contact angle and emulsifying properties, were improved significantly. Confocal laser scanning microscopy and transmission electron microscopy consistently observed WPI-COS tightly adsorbed at the oil-water interface, with smaller emulsion droplets, more uniform distribution and thicker interfacial films at the oil-water interface in WPI-COS microgel particles with sonication-induced unfolding. This investigation demonstrated the feasibility of conformational regulation of interfacial proteins in tuning techno-functional features of microgel particles.