Emulsion hydrogels are structurally composite materials combining the advantages of emulsions and hydrogels with the ability to accommodate hydrophobic and hydrophilic components in one system. It is a promising strategy for the excellent encapsulation and delivery of many bioactive ingredients. In this work, the thyme oil-loaded zwitterionic emulsion hydrogels are constructed by the cellulose acetoacetate-horseradish peroxidase-hydrogen peroxide-initiated (CAA-HRP-H2O2-initiated) ternary enzyme-mediated polymerization of the thyme oil-in-water (O/W) emulsions stabilized by cellulose acetoacetate (CAA). CAA is the key component in the system, acting as the emulsifier and the polymerization mediator simultaneously. The formed zwitterionic poly(sulfobetaine methacrylate) (PSBMA) hydrogel network provides emulsion hydrogels with good hydration capacity and potential anti-fouling performance. The thyme oil-loaded zwitterionic emulsion hydrogels exhibit interconnected, uniform, and adjustable porous structures with tunable mechanical properties, antifouling performance, good biocompatibility, and excellent antibacterial activity against S. aureus and E. coli. These results all demonstrate that the ternary enzyme-mediated polymerization of zwitterionic monomers in the continuous phase of O/W emulsion templates is a facile and efficient strategy to encapsulate hydrophobic bioactive ingredients.