Egg white proteins (EWP) were prone to thermal aggregation under heat sterilization conditions, thereby limiting their application in the field of protein beverages. In this study, EWP were microgel particleized via polysaccharide-protein phase separation to enhance their resistance to thermal aggregation during processing. Results indicated that the charge characteristics of polysaccharides were crucial factors influencing their interaction with EWP. Microstructural and physicochemical properties indicated that egg white protein microgel particles (EMGP) with the bilayer structure formation (polysaccharide shell layer and dense protein core) could only be formed in the phase separation system of EWP and anionic polysaccharides (carboxymethyl cellulose sodium salt (low viscosity), carboxymethyl cellulose sodium salt (high viscosity), High-methoxyl pectin). Additionally, the EMGP exhibited uniform size, high denaturation extent and dense structure that effectively prevented structural unfolding and exposure of active sites upon reheating of the EWP. The thermal denaturation temperatures of the EMGP were significantly higher (up to 155.8 °C, 163.5 °C, 165.7 °C), compared to natural proteins (88.8 °C). Thermal stability experiments confirmed that the suspension of 5% w/v microgel particles maintained good flow ability after heating at 100 °C for 30 min, demonstrating excellent thermal stability suitable for high-temperature pasteurization conditions. Moreover, its uniform particle size and adsorption of polysaccharides improved storage stability. In contrast, groups other than anionic polysaccharides exhibited aggregation and gelation upon heating. Overall, this study demonstrated that preparing heat-stable EMGP effectively reduces aggregation in EWP beverages during heat-pasteurization, enhanced product sensory attributes, extended shelf-life, and expanded the application scope of EWP.