The invention discloses a method for screening a transgene sample transfected with a target gene. The method comprises the following steps: 1) carrying out a three-dimensional arrangement setting for a sample group to be detected according to the following methods: setting m rows along the X direction, setting n columns along the Y direction, setting p layers along the Z direction, wherein each layer has m rows and n columns; 2) carrying out the following PCR amplification reactions that: DNA or RNA of all the samples to be detected in each layer are mixed to obtain p mixtures, each mixture is the mixture containing m*n samples; each mixture is independently adopted as a template of the PCR reaction so as to carry out p PCR reactions; if none of the target PCR products is obtained through the p PCR reactions, a case that the sample group to be detected do not contain the transgene sample transfected with the target gene, is confirmed alternatively. According to the method provided by the present invention, the number of the PCR reaction is substantially reduced; time and labour are saved; cost is saved.