The invention discloses a method for processing a harmonic reducer flexible wheel. The method sequentially includes processes of blanking, forging and shaping, normalizing for heat treating, spinning, turning in a CNC (computer numerical control) lathe, gear-shaping in a CNC milling machine and punching and shaping. The process of punching and shaping is performed through matching of a punching machine and a punching and shaping die, an upper die base, an upper padding plate, an upper fixing plate, a lower die base, a lower padding plate, a lower fixing plate, an upper shaping die, a positioning column, a pressing plate, a tightening ring, a tightening-ring pressing plate and a locking screw are arranged on the punching and shaping die, and an inner shaping gear hole is formed in a core portion of the upper shaping die. The pressing plate clamps and fixes a fixed portion of the semi-finished flexible wheel, the positioning column, the tightening ring, the tightening-ring pressing plate and the locking screw cooperatively fix a center hole of the semi-finished flexible wheel, and the inner shaping gear hole performs shaping upon a profile of an outer gear portion. Therefore, flexible-wheel processing can be completed through a universal machine tool, financial burden of manufacturers can be reduced on one hand, and on the other hand, processing precision of the flexible wheel can be guaranteed.