The invention provides a method for improving aluminum-zirconium-based amorphous alloy friction stir welding joint strength. The position of a welding tool is changed according to different welding parameters; correspondingly, the distance advancing side material and the distance from the axis of the welding tool to the weld are adjusted to ensure the materials at the two sides of the weld to make coordinated flow deformation and to be evenly mixed without rough amorphous grains in the weld, preventing the amorphous alloy from crystallization or chemical reaction with aluminum due to overheating; thus an ideal weld microstructure and a stable joint performance are realized.