Abstract: In order to improve the stability of phycocyanin's blue pigment in food processing and solve the bottleneck of its deactivation and fading due to heat, light, and pH changes, this study extracted phycocyanin via a metal ion (Na⁺, Mg²⁺, Mn²⁺, Cu²⁺, Zn²⁺, Fe³⁺) pre-stabilization freeze-thaw method to form binary complexes. Through analysis of pigment preservation rate and stability, Zn²⁺ and Fe³⁺ were identified as the optimal ions for color protection. Subsequently, ellagic acid (EA) was introduced to form ternary complexes, enabling the construction of emulsions. The effect of metal ion-EA modification on the stability and functional characteristics of phycocyanin was investigated. The results indicated that in the binary complex systems, Zn²⁺ (0.06 mol/L) provided the optimum color protection for phycocyanin. After heat treatment at 70 ℃, the pigment retention rate of the phycocyanin-Zn²⁺ complex (PC-Zn²⁺) was 59.89%, which was significantly higher than that of untreated phycocyanin (41.45%) (P<0.05). Low concentrations of Fe³⁺ (<0.02 mol/L) also conferred a protective effect on phycocyanin, albeit with lower efficacy than Zn²⁺. The further introduction of EA significantly enhanced performance. The PC-Zn²⁺-EA ternary complex achieved a pigment retention rate of 63.44% after 70 ℃ heat treatment, with markedly improved thermal stability, antioxidant activity (DPPH radical scavenging rate of 77.03%), and its emulsifying activity increased to 34.67%. Similarly, the PC-Fe³⁺-EA ternary complex also exhibited significant improvements in pigment retention rate (57.60%) and antioxidant activity compared to native PC. This study revealed the stabilizing mechanism of metal ions and polyphenols on phycocyanin via coordination bonds, hydrophobic interactions, and antioxidant synergy. The selected metal ions and polyphenols are food-grade ingredients and were used within safe limits. These findings provide a safe and effective composite strategy and theoretical basis for developing highly stable natural blue pigments and their application in thermally processed foods.