Poor stability and low solubility of flavonoids extremely limited their efficient application in functional foods. Hydrogel delivery systems have good stabilizing and enhancing effects on flavonoids. Apigenin has a variety of biological activities and can be used to treat various inflammatory conditions. However, its low water solubility significantly hinders its widespread applications. As an amphoteric electrolyte, collagen can form a hydrogel delivery system with varying loading ability under different concentrations and pH values. Therefore, five different collagen concentrations and five different pH values were selected to investigate the optimal conditions for incorporating apigenin. Results found that when the collagen concentration was 5 mg/mL and the pH was 9, the collagen hydrogels had a good encapsulation effect for apigenin. The interaction between apigenin and collagen was primarily driven by hydrogen bonding and hydrophobic interactions. The binding of apigenin altered the conformation and microenvironment of collagen. Molecular docking analysis suggested that apigenin maintained binding stability in the hydrophobic pocket of proteins by interacting with several key residues. The experiments of in vitro digestion revealed the apigenin within that collagen hydrogels had good digestion stability. This study will provide a theoretical basis for the application of apigenin in the collagen delivery system.