Three kinds of melamine-formaldehyde (MF) microcapsules, containing transparent shellac, purple shellac, and yellow shellac as core curing agents, were synthesized via in situ polymerization, and then were embedded into the water-based acrylic resin coatings according to the concentrations of 0, 3.0%, 6.0%, 9.0%, 12.0%, and 15.0%, respectively, to obtain waterborne films with different microcapsule contents. The color of different shellacs was relevant to the color parameters of the self-healing waterborne film. The content of microcapsules was negatively correlated with the chromatic aberration of the surface of waterborne films. When the content of microcapsules was 0–6.0%, the chromatic aberration of waterborne films was relatively low. The content of microcapsules and the color of the different shellacs would affect the light transmittance of waterborne films. Among all samples, the light transmittance of the waterborne film containing 3.0% transparent shellac microcapsules was the highest. The microcapsules with different colors of shellac in waterborne films had different self-repairing effects. When the content of microcapsules did not exceed 6.0%, the tensile repair rate of the waterborne film containing yellow shellac encapsulated microcapsules was the highest, at 47.19%. The scratch experiment illustrated that the scratch width of the waterborne coating with yellow shellac microcapsules decreased most significantly, and the width change rate was 73.0% after 5 days. The coating containing the 3.0% yellow shellac microcapsule has the best comprehensive performance on optical and self-healing properties. Exploring the influence of shellac resin’s color and the microcapsules’ content on the waterborne film provides technical references for the application of shellac in waterborne coatings and contribute to the further development of the preparation process of self-healing coatings.