The invention discloses a method for improving refining efficiency of a magnesium zirconium grain refiner by friction stirring processing. The method comprises the steps of (1) clamping commercial Mg-Zr intermediate alloy on a friction stirring welding machine; (2) performing friction stirring processing on an Mg-Zr intermediate alloy sheet in a multi-pass gradual shifting type, and covering the whole material through a processing area; and (3) cutting the Mg-Zr intermediate alloy processed by friction stirring into small blocks; adding the small blocks to a melt based on the required quantity, thus realizing the grain refining of a magnesium alloy. The method is stable and reliable in processes, low in cost, environmentally friendly, and outstanding in effect; the Mg-Zr intermediate alloyis processed by FSP (friction stirring processing) and the magnesium alloy is subjected to grain refining test, thus about 30-40% of quantity of Zr is saved on the basis that the qualified grain refining effect is achieved.