The invention relates to a method of immobilizing DNA on gel, in particular to a DNA immobilization method based on immobilization of nucleic acid on the gel and the application thereof. The immobilization method of a DNA sample comprises three steps of raw material selection, mixing and polyreaction. In the step of raw material selection, the selected raw materials and dosage are as follows: 10 percent of 10*TBE(pH13), 10-70 percent of 40 percent methacrylamide storage liquid, 1muL-5ml diluted degeneration amino terminal modified nucleic acid, 1-10 percent of N, N, N, N-tetramethyl ethylenediamine, 1-10 percent of 10 percent ammonium persulfate, and water. In the step of mixing, configured gel raw material is added with amino terminal modified nucleic acid to be mixed. The nucleic acid amount in the mixture is 10-1,000ng/3muL. In the step of polyreaction, 5muL mixture is put in a PCR reaction tube at 37 DEG C for 30min. After the polyreaction is finished, the mixture is molded into gel shape, and the amino terminal modified nucleic acid is immobilized by the polyreaction in the gel. The method has the advantages of high bearing capacity, immobilization of the terminal modified nucleic acid molecule by stable covalent bond formed between the molecule and a solid phase carrier and capacity of enduring dramatic conditions of the PCR reaction, etc.