Menthol and thymol, as natural antiseptics, have the advantages of nontoxicity and broad-spectrum antimicrobial activity, which solves the problems of antibiotic resistance and toxicity of metal antiseptics. However, their practical applications face the challenges of chemical instability and difficult solubility in water. In this study, menthol and thymol were tactfully physically combined, forming hydrophobic deep eutectic solvent (HDES), which were then encapsulated via an emulsion system to address their instability and hydrophobicity. Then, 2-hydroxyethyl acrylate was added and polymerized into a covalent network to fabricate a HDES-loaded heterogeneous gel, featuring sustained-release characteristics for the preservation of perishable fruits. The combination of emulsion encapsulation and gelation improves the stabilization of menthol and thymol, allowing for delayed release and providing materials with a 34-day antibacterial cycle. Additionally, the emulsion gel presents tensile strain as high as 2250%, making it appropriate as practical packaging materials. Through cherry, tomato, and broccoli preservation tests, it is found that compared with the monomer such as thymol, menthol, and the deep eutectic mixture, the emulsion gel presented the best antibacterial activity, enabling the preservation days to significantly increase. We calculated that it was probably due to the HDES and cross-linking network displaying a synergistic effect. This design will provide a perspective for the preservation of perishable fruits and vegetables.