The preparation of active packaging materials from chitosan (CS), cellulose nanocrystals (CN), and epigallocatechin gallate (EGCG) involved a complex multi-component system that was highly susceptible to phase separation or aggregation of active components. This necessitated the urgent development of multi-component compatibility matching models and novel interfacial regulation strategies to stabilize the system and ensure homogeneous distribution of functional constituents. This study employed a pre-constructed EGCG-loaded CS/CN nanocrystal hydrogel (EGCG hydrogel) as the model system. The morphological and structural characteristics of the layer were systematically characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FT-IR). Subsequently, molecular dynamics (MD) simulations were conducted with parameterized force fields to analyze the conformational dynamics and intramolecular/intermolecular interactions within the composite hydrogel system. The results demonstrated that the CS/CN nanocrystal hydrogel serves as an effective carrier for EGCG. With EGCG incorporation, the material surface exhibited increased roughness, thicker pore walls, and a more compact overall structure compared to the pristine hydrogel. Additionally, the EGCG hydrogel retained only a broad diffraction peak at 20.0° in XRD patterns, while the characteristic sharp peaks of pure EGCG disappeared, indicating the loss of crystalline EGCG domains within the matrix. Crucially, no new covalent bond-associated peaks emerged in the FT-IR spectra, confirming that EGCG was physically entrapped via non-covalent interactions rather than chemical bonding. MD simulations further revealed that increasing EGCG loading enhanced system stability, as evidenced by reduced fluctuations in root mean square deviation (RMSD) and solvent-accessible surface area (SASA). The radius of gyration stabilized at approximately 7 nm, suggesting a consolidated molecular conformation. Moreover, the number of hydrogen bonds between CN and CS increased significantly upon EGCG addition, implying that EGCG molecules reinforce interfacial interactions within the composite network through hydrogen-bond-mediated crosslinking. This study provides a theoretical foundation for the rational design and precise fabrication of controlled-release active packaging materials.