The invention discloses a method for preparing an aluminum-scandium intermediate alloy by using calciothermy. The method comprises the following steps of: (1) calculating the weights of halides of aluminum, metal calcium and scandium serving as raw materials, or scandium-containing fused salt, anhydrous calcium chloride and alkali chloride required for smelting in each furnace according to the component content of the aluminum-scandium intermediate alloy; (2) after uniformly mixing a flux, adding the flux into a crucible to smelt; (3) when the flux is completely smelted, adding scandium halide and preserving the heat in a closed protective atmosphere; (4) adding aluminum and metal calcium into the smelted scandium-containing fused salt, preserving the heat and thermally reducing for 20 to 200 minutes; (5) after finishing the thermal reduction reaction, slagging off, and adding an excessive amount of refining agent to remove the calcium, when the calcium content in the alloy is less than 50ppm, casting an ingot and cooling, and performing water leaching to remove slag so as to obtain the aluminum-scandium intermediate alloy. The method disclosed by the invention has the advantages of low fluorine, micro discharge, easiness in operation, steady aluminum-scandium alloy product, novelty and economy.