The invention relates to the technical field of coatings, specifically to a baking type waterborne acrylic coating composition with excellent thixotropy and a preparation method thereof. The coating composition provided by the invention is prepared from the following main raw materials by weight: 0.05 to 0.45% of a functional filling material A, 10 to 15% of deionized water, 30 to 38% of tertiaryamine group containing hydroxyl-functionalized waterborne acrylic resin, 2.5 to 4.5% of waterborne amino resin, 4.5 to 8% of a cosolvent A, 0.1 to 0.8% of a dispersant, 0.1 to 0.55% of a leveling agent, 0.1 to 0.65% of an anti-foaming agent, 0.05 to 0.4% of a pH regulator, 5 to 15% of a pigment, 10 to 40% of a filling material B, 0.1 to 0.85% of a rheological auxiliary agent and 3.5 to 9.7% of a cosolvent B, wherein the functional filling material A is hectorite or flaky silicate. The coating provided by the invention has excellent thixotropy, sag resistance and stone-bumping resistance.