The invention discloses a method for preparing a manganese-iron alloy based on low-grade manganese ore. The method comprises four processes, namely ball milling of raw materials, pelletizing, quick reduction and slag-metal separation. The method comprises the following steps: mixing low-grade manganese ore and iron ore powder; milling the mixed ore, and screening with a 150-300 meshes screen; mixing the screen underflow with the pulverized coal, lime, bentonite and water, and pelletizing on a disc type pelletizer, wherein the diameter of the green balls is 10-16mm; drying the green balls at 105 DEG C for 4h; reducing the dried pellets at 1,450-1,550 DEG C for 8-15min; and after the reaction, crushing the raw material, and performing simple magnetic separation to obtain granular manganese iron, wherein the manganese content is 45-70%, the iron content is 25-45%, the carbon content is 2-5%, and the balance is impurities. According to the method disclosed by the invention, the manganese-iron alloy is prepared by the one-step process of the quick reducing technology, the slag and metal are easily separated, the process is pollution-free, the manganese recovery rate is high, and high value-added utilization of the low-grade manganese ore is realized.