An embodiment of the invention discloses a copper column structure packaging substrate and a processing method thereof, which are used for solving the problem of a copper column structure in the prior art, so that the copper column structure on the copper column structure packaging substrate has the advantages of high uniformity and high strength. The processing method comprises the steps of: providing a circuit board, wherein the circuit board is provided with a substrate, a second copper layer and a super-thick dry film, and the super-thick dry film is arranged on one surface of the circuit board; drilling a hole in the circuit board to form a copper column through hole, and forming a first copper layer on the inner wall of the copper column through hole; forming a copper column in the copper column through hole by adopting an electrocoppering process; and removing the super-thick dry film, the second copper layer and exposed part of the first copper layer to obtain the copper column structure packaging substrate.