The invention discloses a natural antibacterial eugenol microcapsule and a preparation method thereof. A shell material of the natural antibacterial eugenol microcapsule is a composite shell material consisting of polyurethane and alkali lignin, a core material of the natural antibacterial eugenol microcapsule is eugenol, and the eugenol-encapsulated microcapsule is prepared through a Pickering emulsion method and interfacial polymerization. The shell material is an isocyanate-based polymer raw material which is wide in source, low in cost and easy to obtain, and the core material eugenol is a natural volatile oily substance and has broad-spectrum and high-efficiency antibacterial performance. The microcapsule prepared by the invention is micron-sized, has higher sphericity and has higher eugenol encapsulation efficiency. The natural antibacterial eugenol microcapsule disclosed by the invention has a potential long-acting antibacterial effect through slow release of eugenol. Microencapsulation of eugenol changes eugenol into a solid powder structure from a liquid state, and the eugenol microcapsule has wide application potential in application of antibacterial materials and packaging materials.