The invention discloses a high-strength and water-resistant desulfurization building gypsum self-leveling material and a preparation method thereof. The self-leveling material comprises the following raw material components and content, wherein a raw material comprises a main material and an auxiliary material; the main material comprises 50-70% of desulfurization building gypsum, 6-10% of cement, 20-40% of slag and 0-20% of fly ash; and the auxiliary material comprises 0-6% of steel slag, 0.1-0.4% of special gypsum water reducing agent, 0.1-0.4% of retarder, 1-4% of gypsum whisker, 0.05-0.1% of rubber powder and 0-40% of sand ratio according to the mass percentage of the main material. The preparation method comprises the following steps of mortar preparation and mortar body preparation, wherein in the step of the mortar preparation, various raw materials concerned with the self-leveling material are pulverized according to a limited proportion and mixed uniformly in a ball mill to form powder; and in the step of the mortar body preparation, water is added to the prepared powder according to a mass ratio of the water to the powder obtained in the step of the mortar preparation of (0.3:1)-(0.4:1), uniform stirring is performed, and then a defoaming agent is added. The self-leveling material has high strength and high water resistance.