Whey protein isolate (WPI) was dietary protein with various functional properties and nutritional value, while anthocyanins were famous for their biological activities. This study aimed to investigate the effect of the interaction between WPI and rose anthocyanin extract (RAEs) at pH7.0 and pH9.0 on the structure, emulsification, and digestibility of WPI. The results showed that compared with the initial WPI, all WPI-RAEs complexes presented lower hydrophobicity and free SH content, higher absolute ζ-potential, thermal stability, and emulsification. In addition, the interaction of WPI and RAEs could reduce the digestibility of WPI. More importantly, WPI-RAEs complexes may be more effective emulsifiers than the original WPI, which was of great value to the dairy processing industry and food nutrition.