A new kind of bifunctional microcapsule containing a n-octadecane (OD) and thyme oil (TO) core based on polyurea shell designed for thermal energy storage and antibiosis was prepared successfully through interfacial polymerization. The scanning electron microscopic investigations reveal that the obtained composite microcapsules present the regular spherical morphology and the transmission electron microscopic observations confirm the clear core-shell structure. Morphological and chemical structure analyses prove the successful synthesis of bifunctional microcapsules. Thermogravimetric analysis indicates that the polyurea shell can protect the composite cores effectively. Differential scanning calorimetry examination shows that the bifunctional microcapsules can maintain high thermal storage capacity and the encapsulation efficiency of OD increases with the increase in TO. The supercooling crystallization can be notably suppressed by adding 7 wt.% of n-octadecanol. A study on the release behavior of TO from the bifunctional microcapsules reveals that the Higuchi kinetic model could better fit the TO release profile. The antibacterial results demonstrate that the bifunctional microcapsules can effectively inhibit the growth of Staphylococcus aureus and the inhibition rate can reach as high as 99.9% when the mass concentration of microcapsules is over 3 wt.%.