The invention relates to hydration resistant magnesia-calcium clinker and a preparation method thereof. The technical scheme comprises the following steps: when granular magnesia-calcium clinker sintered by a high-temperature calcination method is continuously dynamically cooled to 100-300 DEG C, thermal insulation is carried out for 1-5 min; and organic silicone resin is continuously sprayed onto the surface of the granular magnesia-calcium clinker under the same temperature condition, and the granular magnesia-calcium clinker is cooled to room temperature at the speed of 5-10 DEG C/min after the spraying, so as to obtain the hydration resistant magnesia-calcium clinker. 1-5kg of the organic silicone resin is sprayed onto each ton of the magnesia-calcium clinker, and spray amount per unit time of the organic silicone resin is 0.05-1 kg/s. Particle size of the granular magnesia-calcium clinker is 1-20 mm. The granular magnesia-calcium clinker comprises the following main chemical components: 52-55 wt% of Cao, 42-46 wt% of MgO and SiO2+Al2O3+Fe2O3 being less than or equal to 3 wt%. The production cost is low; preparation technology is simple; and energy consumption is low. The prepared magnesia-calcium clinker has good hydration resistance, high high-temperature strength and erosion resistance, and will not pollute molten steel.