In this paper, urea-formaldehyde resin microcapsules with shellac resin as core material were prepared by in-situ polymerization. Morphologies of shellac resin microcapsules were characterized by optical microscope (OM) and scanning electron microscope (SEM). Both microcapsules were spherical in shape. The encapsulation property of shellac resin was proved by Fourier transform infrared (FTIR). Shellac resin microcapsules and fluorane microcapsules were added to waterborne primer or topcoat at the same time to prepare waterborne coatings with thermochromic and self-healing dual functions. The effects of microcapsules on optical properties, mechanical properties, self-healing properties, anti-aging performance, and thermoreversible discolouration mechanism of coating films were studied. These results showed that the topcoat with 10.0% fluorane microcapsules and 5.0% shellac resin microcapsules had a better comprehensive performance. At this time, the colour of coating transformed yellow into colourless at 32 °C, and it had a good colour recovery. Shellac resin microcapsules endowed the coating with self-healing performance, and the self-healing rate was 35.9%. The research results provide a reference for the progression of multifunctional wood coatings.