The effects of quantum dots (QDs) on the elimination of nonspecific amplification of the polymerase chain reaction (PCR) were investigated. It was found that QDs could increase the specificity of the PCR at different annealing temperatures and with DNA templates of different lengths. The effects of QDs on the efficiency of the PCR were also studied, and the results showed that there was no enhancement. The mechanisms underlying, these effects are discussed. This method could be used to modify the amplification results of the conventional PCR. Furthermore, this technology could make the PCR more widely applicable, especially in the multi-PCR reaction system with different annealing temperatures. This is of great significance for gene diagnosis.