The invention relates to a stirring tool for non-flash friction stir welding and a welding method thereof. A shaft shoulder of the stirring tool is provided with at least two blades in the circumferential direction. The welding method comprises the steps that the stirring tool for non-flash friction stir welding is machined; a clamping part of the stirring tool for non-flash friction stir weldingis assembled to a spindle of a welding machine; a stirring needle rotates to be inserted into a to-be-welded workpiece, and the welding indentation amount of the shaft shoulder is adjusted for welding; and after welding is completed, the workpiece and the stirring tool for non-flash friction stir welding are disassembled. Through, the stirring tool for non-flash friction stir welding and the welding method thereof, flashes generated in the welding process are milled, the welding and flash removing procedures are combined into one procedure, and the production efficiency of friction stir welding is improved.