Abstract: To enhance the application of rutin and lysozyme in the food industry, a rutin-lysozyme complex was formed, and rutin-lysozyme microcapsules were subsequently prepared via spray drying. In this study, the interaction between rutin and lysozyme was initially investigated using molecular docking and molecular dynamics. Then, the optimal preparation conditions for the rutin-lysozyme microcapsules were determined. Finally, the microcapsules were characterized. The results showed that rutin and lysozyme could form a stable complex through hydrogen bonding and other interactions. The optimal preparation conditions for the rutin-lysozyme microcapsules were as follows: A wall material ratio of 1:2, a core-to-wall ratio of 1:2, a homogenization rate of 9000 r/min, and a drying temperature of 170 ℃. The particle size and zeta potential results indicated good dispersion stability of the microcapsules. The three-dimensional fluorescence and infrared spectroscopy results suggested that interactions between the core and wall materials led to the formation of additional hydrogen bonds. Scanning electron microscopy revealed that the microcapsules had a smooth and crack-free surface. The results of the in vitro digestion simulation test showed that after the rutin-lysozyme complex was subjected to simulated gastric and intestinal digestion, the DPPH radical scavenging rates were 21.4%±1.21% and 18.64%±0.6% respectively, and the antibacterial rates were 28.02%±2.32% and 13.01%±0.61% respectively. However, after encapsulation, the DPPH radical scavenging rates significantly increased to 41.43%±1.03% and 34.09%±0.9% (P<0.05), and the antibacterial rates increased to 31.04%±1.4% and 21.95%±1.22%, indicating that the microcapsules could effectively protect the antioxidant and antibacterial activities of the rutin-lysozyme complex. In addition, the release kinetics model of the microcapsules showed that the release mechanism parameter at 4 ℃ was 0.93, which was between the diffusion-limited kinetics (0.54) and the first-order reaction kinetics (1.00), indicating that it could effectively release the rutin-lysozyme complex in a sustained manner under low-temperature conditions. In conclusion, this study is expected to provide new research ideas for the application of natural active ingredients in the food field.