The invention discloses a PCR (polymerase chain reaction) method for eliminating genes, which can eliminate non-target genes in a mixed gene population. The key points of the technology disclosed by the invention are as follows: making or artificially synthesizing the non-target genes into short-sequence gene eliminating primers, performing enzyme cutting on the mixed gene population containing target genes, adding a restriction enzyme cutting site with a base pair mismatch and a joint with Poly (dA), purifying, using the mixed gene population as a template, restoring the correct enzyme cutting site through the gene eliminating primers and annealing extension of the template in the PCR, and then using the heat-resistant restriction enzyme cutting site to eliminate the joint of the non-target genes so as to prevent amplification of the non-target genes. The reaction is cycled by utilizing a PCR instrument: 30s at the temperature of 94 DEG C, 40s at the temperature of 60 DEG C, 8min at the temperature of 75 DEG C, 12-18 cycles are performed for enriching the target genes, and then the conventional PCR is adopted for further amplifying the target genes. The method disclosed by the invention has the advantages of high efficiency, high speed, simplicity and convenience in operation, low cost, high repeatability, good separation effect and low false positive rate.