The antibacterial microcapsules were prepared by encapsulating Toddalia asiatica (L.) Lam. extracts with urea–formaldehyde resin. The orthogonal test was designed to investigate the effects of the mass ratio of core and wall materials (Wcore:Wwall), emulsifier concentration, reaction temperature and reaction time on the yield rate and coverage rate of microcapsules, and to obtain the best preparation technology for microcapsules. The single-factor results indicated that the maximum influence factor was the Wcore:Wwall of the microcapsules; the larger the Wcore:Wwall, the easier the microcapsules were to agglomerate; and when the Wcore:Wwall was 0.8:1, the coverage rate reached the maximum value of 11.0%. The waterborne topcoat paint film was prepared by adding the microcapsules in the same content. The yield rate, coverage rate, and microscopic morphology of Toddalia asiatica (L.) Lam. extract microcapsules were analyzed, as well as the effects of microcapsules on the microscopic morphology, optical properties, cold liquid resistance, mechanical properties and antibacterial properties of a waterborne topcoat paint film. Combining the optical properties, cold liquid resistance, physical properties, and antibacterial properties of the waterborne topcoat paint film, the comprehensive performance of the waterborne topcoat paint film with the Wcore:Wwall of 0.8:1 was superior. The gloss was 8.07 GU, color difference ΔE was 9.21, visible light transmittance was 82.90%, resistance to citric acid, ethanol and detergent were grade 1, 2 and 2, respectively, elongation at break was 15.68%, and roughness was 3.407 µm. The antibacterial activity against Escherichia coli and Staphylococcus aureus were 42.82% and 46.05%, respectively. In this study, a waterborne topcoat paint film with a microcapsule-coated plant-derived antibacterial agent as the core was prepared, expanding the application prospect of plant-derived antibacterial microcapsules.