The melamine/rice husk powder-coated shellac microcapsules were prepared by in-situ polymerization with melamine resin mixed with rice husk powder as microcapsule wall material and shellac as microcapsule core material. The effect of the addition amount of microcapsules with different wall material ratios on the performance of wood waterborne primer coating was investigated. The results show that the most important factor affecting the performance of microcapsules is the content of rice husk powder. Through the preparation and analysis of shellac microcapsule primer coating coated with melamine/rice husk powder, when the content of microcapsule powder is 0–6%, it has little effect on the optical properties of wood waterborne primer coating, and the microcapsule with 5.5% rice husk powder has little effect on the color difference of primer coating. The coating hardness increases with the increase of rice husk powder content in wall material. When the rice husk powder content in wall material is more than 5.5%, the coating hardness reaches the best. When the content of microcapsule powder is 3.0–9.0%, the adhesion of the coating is better, and the coating with rice husk powder content of 5.5% in microcapsule wall material has better impact resistance. When the content of rice husk powder was 5.5% and the content of microcapsule powder was 6%, the elongation at break of the primer coating was the highest and the tensile resistance was the best. The composition of wood waterborne primer did not change after adding microcapsule. The water-based primer with microcapsule has better aging resistance. The water-based primer coating with rice husk powder content of 5.5% and the addition amount of 6% had the best comprehensive performance, which lays the technical reference for the toughness and self-repairing of the waterborne wood coatings.