The invention discloses a compound treatment purifying method of a magnesium alloy melt. The method comprises the following step: carrying out gas blowing stirring treatment while purifying the magnesium alloy melt by a refining flux, wherein the refining flux can purify and remove bigger inclusions of the magnesium alloy melt, and meanwhile, bubbles of inert gases or nitrogen introduced by gas blowing stirring enable the inclusions suspended in the magnesium alloy melt to quickly come up to the surface of the melt, so that inclusions in the magnesium alloy melt are effectively removed, particularly fine inclusions, thereby improving the quality of a magnesium alloy to a great extent. Furthermore, the method further promotes homogenization of magnesium alloy components, improves the yield of a zirconium refiner and controls segregation of zirconium element. Therefore, the method disclosed by the invention has the compound purifying and refining functions, and is short in treatment time, simple and suitable for experimental and industrial applications.