Biochip technology which had emerged from the fusion of biotechnology and micro/nanofabrication technology at the end of 1980s has been widely used in life science, medicine, clinical diagnosis, drug development, agriculture, environmental protection and strategies. DNA microarray (also call gene chip, DNA chip), one kind of biochips, is small chip containing many oligonucleotide probes. It can hybridize with labelled sample, making it possible to detect large numbers of oligonucleotides at one time. So DNA microarray can overcome the disadvantage of traditional hybridization technology such as complexity, low automation, poor efficiency and quantity of molecules detected. This paper describes a new method to detect transgenic plant with gene chip. We have developed a novel arrayed-primer extension technique. It combines hybridization and PCR in one step, while ordinary DNA microarray needs two separate steps. Therefore our method provide a feasibility to detect long DNA fragment .