Anthocyanins (ACNs) are widely used in the culinary, cosmetic, and biomedical industries owing to their potent bioactivities. However, the rapid degradation of ACNs in extreme environments is a major limiting factor for their physicochemical stability and bioactivity. This study reported a facile and environmental-friendly ACN embedding strategy using chondroitin sulfate (CS) and whey protein isolate (WPI) to prepare the CS/WPI@ACN complex. The encapsulation efficiency of CS/WPI@ACN reached up to 84.87 % when the CS-to-WPI mass ratio was 1:5, and the core-to-wall material ratio was 1:3. Molecular docking analysis revealed that the CS/WPI complex harbored a concave chamber, which was conducive for the embedding of small ACN molecules and promoting drug activity. The CS/WPI@ACN complex enabled sustained ACN release in the gastrointestinal tract in vitro. The CS/WPI@ACN complex was stable under ascorbic acid treatment conditions, high temperatures, and a wide range of pH levels. In vitro release data demonstrated that most encapsulated ACNs were released in the small intestine. Furthermore, the antioxidant activity of the CS/WPI@ACN complex was higher than that of free ACN. Therefore, this study proposed a strategy to protect unstable active substances, and laid a foundation for blueberry anthocyanins in the high-value utilization of functional drinks.