According to the plasmid map of genetically modified soybean(Roundup Ready), three exogenous gene( CaMV35S promoter, NOS terminator, NOS/EPSPE gene) and one endogenous gene ( Lectin ) were selected as target genes to design and synthesize their primers. The probe was synthesized using the method of nick translation and labeled with DIG dUTP. Multiplex PCR was used to amplify the target sequence in soybean sample DNA, then the DNA chips were hybridized with PCR product, at last the chips displayed the hybridization result. The DNA chip for identifying genetically modified soybean was highly specific and reproducible and its sensitivity was 0 5%,meanwhile the detection efficiency was highly improved with the use of multiplex PCR. So genetically modified soybean could be detected and identified rapidly and correctly.