In this paper, a chitosan-modified nano-silver solution was used as the core material of an antibacterial agent, and melamine formaldehyde resin was coated onto the core material to obtain the antibacterial microcapsules. The core/wall ratio, the stirring rate, the mass ratio of chitosan to silver ions, and the concentration of the emulsifier were used to carry out four-factor and three-level orthogonal experiments to explore the most significant factors affecting the coverage rate and output of microcapsules and the best preparation technology. The results showed that the concentration of the emulsifier was the most important factor affecting the preparation of microcapsules. The higher the concentration of the emulsifier, the better the dispersed morphology of microcapsules, and the higher the coverage rate, up to 44.0%. The antibacterial coating was prepared by mixing microcapsules with a waterborne primer at a content of 4.0%. Its optical properties, mechanical properties, and antibacterial properties were analyzed. By increasing the concentration of the emulsifier, the gloss of the coating showed a trend of first increasing and then decreasing. When the emulsifier concentration was 2.0%, the gloss of the Andoung wood surface coating reached the maximum value of 21.23%. The influence of emulsifier concentration on the color difference of coating had no obvious law, and it was negatively related to the light transmittance. In terms of mechanical properties, the concentration of the emulsifier is directly proportional to the hardness and impact resistance of the coating, with the maximum reaching 31 kg·cm, and is negatively related to adhesion and roughness. In terms of antibacterial properties, the higher the concentration of the emulsifier, the better the antibacterial properties of the coating. When the concentration of the emulsifier was 4.0%, the antibacterial rates of coating which coated the glass substrate were 71.3% and 80.0% for Escherichia coli and Staphylococcus aureus, respectively. The antibacterial rates of the Andoung wood surface coating reached the maximum, which were 68.4% and 73.2%, respectively, and the antibacterial performance was excellent. In this study, an efficient antibacterial microcapsule for waterborne coatings was prepared, which provided the reference value for the application of antibacterial microcapsules in waterborne coatings.