The present invention relates to a method for welding a 3D bellows. The method includes: repeatedly laminating a unit cell material, a second adhesion-preventing film, a different unit cell material, and a first adhesion-preventing film; forming ventilation holes on the unit cell materials by pressing a hole-processing cutter on which a hole-circumference welding heater is installed onto the laminated unit cell materials and the first adhesion-preventing films, and then heating the circumference of the ventilation holes; finishing two sides of the unit cells by positioning, on two outermost surfaces of the laminated unit cell materials, a first finishing unit cell material and a second finishing unit cell material provided with an air injection port; and cutting the first finishing unit cell material, the unit cell materials, and the second finishing unit cell material and heating the periphery of the cut area by pressing a contour-processing cutter.