The invention relates to a method for manufacturing a guide groove of a servomotor cylinder of a runner cone of a hydroturbine. The method is characterized in that a boring lathe workbench is provided with two V-shaped irons; a regulating parallel is arranged under each V-shaped iron; small ends of two runner cones are aligned with each other and firmly welded by a butt strap; then, the two runner cones are arranged on the V-shaped irons horizontally, and are fixed after being aligned with a principal axis of a boring lathe in each direction; the principal axis of the boring lathe is provided with a right-angle milling head; and the milling head is provided with an end mill manufacturing guide groove. The method solves the problems of difficult assembly and difficult alignment in manufacturing the guide groove of the runner cones, greatly improves the manufacture accuracy and production efficiency, and has the advantages of easy operation and low manufacture cost.