Summary Ultrasound provides an approach for improving the conjugation efficiency of cyanidin‐3‐O‐glucoside (C3G) and β‐lactoglobulin (βLG), thereby increasing cyanidin stability and imparting some characteristics to proteins. In the present study, the effects of ultrasound on C3G conjugation efficiency was investigated by exploring the binding mechanism and shifts in functional properties. Ultrasound enhanced conjugation efficiency by increasing binding affinity from 5.7 × 105 to 10.6 × 105 m−1, and binding number of C3G from two to three, as well as the maximum peak temperature of C3G from 84.7 to 88.4 °C in βLG–C3G complexes, implying improved C3G thermostability. Furthermore, C3G conjugation imparted antioxidant properties to the complexes, and altered the conformation of βLG, which enhances emulsifying ability and emulsification stability. Such changes further improved conjugation efficiency. The results of this study could facilitate the application of C3G as a natural additive in food products.