The modification experiment of waterborne coating was carried out by adding microcapsules. The wall material of the microcapsule was urea-formaldehyde resin and the core material of the microcapsule was epoxy resin. Core material can improve the toughness of the coating and prevent the cracking of the coating. The influences of different contents of microcapsules and the order of adding microcapsules in the coating process on the properties of gloss, color difference and toughness were studied. The results showed that the gloss of the waterborne coating decreased with the increase of microcapsule content. The color difference of coating increased first and then decreased, and when the microcapsule content was 8.0%, the color difference was the largest. The toughness of the coatings also increased first and then decreased. When the content of the microcapsule was 10.0%, the toughness of the coating was significantly enhanced. When the microcapsules with a content of 10.0% were added to the waterborne coating, under the same process, the coating gloss of microcapsules added to the primer was relatively high, and the coating gloss was the highest when the coating process was three-layer primer and two-layer topcoat. The microcapsule had little effect on the color difference of coating in different coating processes. When the coating process was three-layer primer and three-layer topcoat, the coating toughness was the best when microcapsules were added to the topcoats. This study provides a basis for industrial application of waterborne coatings to enhance their toughness.