Since 1970s, the world paid great attention to the security of Genetically Modified Organism. The area of Genetically Modified Maize was large. According to the plasmid map of Genetically Modified Maize, we select exogenous genes (CaMV35S promoter, NOS terminator, PAT gene, IVS2/PAT, CDPK/CryIA(b), Maize genome/CaMV35S, PAT/CaMV35S!, Cry9C/CaMV35S!) and endogenous gene (IVR) as target genes, 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 maize sample DNA, then we hybridized the DNA chips with PCR product, at last the chips displayed the hybridization result. The DNA chip for identifying Genetically Modified Maize was highly specific and repeatable and its sensitivity was 0.1％, meanwhile the detection efficiency was highly improved with the use of multiplex PCR. So we could detect and identify Genetically Modified Maize rapidly and correctly.