This present invention describes a system of waterproof shoes with thermoplastic polyurethane (TPU) insteps, including vamp, instep and sole, in which the waterproof welt coated with waterproof glue is gummed on the seam between the vamp and the sole; the metal section, instep, mid-sole and inner welt is formed in integration by injecting with TPU polyurethane, in which the outer and inner welts are gummed with glue and sewn firmly with threads on the opposite sides of the instep; a metal piece is put between the thin bottom and the filling materials on the bottom side of the instep. The waterproof methods (the waterproof outer surface of the instep, and the waterproof welt coated with waterproof glue and gummed on the seam between the vamp and the sole reach the purpose of saving the materials and labor, obtaining the waterproof effects which is even better than those of the traditional waterproof shoes and may provide more functionality and better visual effects.