The traditional optimization methods for protein-based packaging materials are plagued by limitations of low efficiency and high cost in meeting the requirements of sustainable packaging. To address this challenge, researchers have introduced molecular docking technology, which can efficiently simulate the interactions between proteins and functional molecules. This technology not only helps to improve the performance of materials, but also provides a scientific theoretical basis for experimental design. In addition, the combination of simulation and experimental verification shows remarkable advantages in enhancing the antibacterial, barrier and mechanical properties of protein-based packaging materials. The application framework of molecular docking technology in protein-based packaging materials is reviewed, and the research results of simulation analysis and experimental verification in gelatin, soy protein, zein, gliadin, as well as casein/whey protein are systematically summarized. Future research priorities should focus on developing higher-precision prediction models, realizing multi-scale simulations, and deepening the integration of simulation and experiments, so as to further promote the intelligent development and industrial application of protein-based packaging materials.