The invention discloses a method for preparing an aluminum-scandium master alloy by thermal reduction of an aluminum-calcium alloy. The method includes the steps as follows: firstly, by the contents of components in the aluminum-scandium master alloy, calculating the weight of the material aluminum-calcium alloy, the halide or the molten salt of scandium, and alkali chloride which are needed for smelting in every furnace; secondly uniformly mixing the halide or the molten salt of scandium with alkali chloride, adding the mixture into a crucible, raising temperature to 750-950 DEG C for melting the mixture, thus obtaining molten salt containing scandium; thirdly, adding the aluminum-calcium alloy into the molten salt containing scandium and after the aluminum-calcium alloy melts, keeping temperature and conducting thermal reduction for 20-200min; and fourthly, after the thermal reduction reaction finishes, adding excessive refining agent to remove calcium; and when the content of the calcium in the alloy is less than 50ppm, pouring and cooling a cast ingot, and then conducting water leaching for deslagging, thus obtaining the aluminum-scandium master alloy. The technology is simpleand feasible in flow, high in metal yield, simpler and more environment-friendly than the traditional method and capable of realizing green production; and the method has the advantages of being simple in operation and equipment, low energy consumption in production, less pollution to the environment and economic stability.