The invention discloses a silver nano column cluster array, as well as a preparation method and application thereof. The silver nano column cluster array comprises the silver nano column clusters covering a gold film, wherein the silver nano column clusters constituting the silver nano column cluster array comprises more than 20 silver nano columns; the diameter and length of each silver nano column are 5-75 nm and 750-850 nm respectively, the distance between the centers of the roots of two columns is 130-170 nm, and the top ends of the more than 20 columns are gathered. The preparation method comprises the following steps: a monolayer crystal template is moved to the surface of a through-hole alumina template, the gold film is sputtered on the monolayer crystal template, then, the monolayer crystal template is placed in a silver electrolyte, the monolayer crystal template is removed after the silver nano columns is subjected to electro-deposition, after the gold film is sputtered on one surface, covering the gold film, of the alumina template, the alumina template is dissolved away, and then the gold film on which the silver nano column cluster array is placed is dried to prepare the objective product, wherein one surface of the alumina template is coated with the gold film, and the silver nano columns are placed in the through holes of the alumina template. The silver nano column cluster array can be used as the active substrate of surface reinforced raman scattering, and a laser Raman spectrometer is utilized to measure polychlorinated biphenyl-3 attached thereon or measure the content of parathion-methyl in an organophosphorus pesticide or the content of 2, 4-D in an organo-chlorine pesticide.