The invention relates to a preparation method of a thorium-based mixed oxide ceramic microsphere. The preparation method comprises the following steps of under the conditions of heating and stirring,adding cerous ammonium nitrate or uranyl nitrate and plutonium nitrate solid into a thorium nitrate solution to form a mixed solution, using ammonium hydroxide to adjust the pH (potential of hydrogen)value to form a hydrolysis solution, adding a thickener (polyvinyl alcohol solution) into the hydrolysis solution, and stirring, so as to form a thorium-based mixed sol solution; enabling an exciterto disperse the thorium-based mixed sol solution into liquid droplets, sequentially sending into an air section and an ammonia gas section, and finally sending into the ammonium hydroxide to form a gel microsphere; heating and aging the gel microsphere in concentrated ammonium hydroxide, alternatively washing by ethyl alcohol and thin ammonium hydroxide, washing by deionized water, flatly paving the single layer of washed gel microspheres in a drying furnace, and leading water vapor to heat and dry, so as to obtain the dried gel microsphere; placing the gel microsphere into a sintering furnace, and heating and sintering in an air atmosphere, so as to obtain the mixed oxide ceramic microsphere. The preparation method has the advantage that the fuel with uniform distribution of elements canbe prepared.