The high-throughput extraction of high-quality genomic DNA is one of the basic analysis of plant molecular biology research, and an important technology for identifying genomic variation of crop germplasm resources, genetic mapping of important functional genes, crop molecular breeding based on genomic marker-assisted selection. However, the efficiency of conventional method is inadequate for large-scale DNA extraction. The automatic high-throughput instruments are expensive and consumables, and the centrifugal-sedimentation method commonly used in laboratories are tedious and involve more organic solvents. To supply the demand of high-throughput, large-scale and less expensive DNA extraction, we have developed a 96-pool magnetic separation device DNA. Using this device, the genomic DNA extraction has been succeeded for wheat, rice, maize and other cereal crops, as well as vegetable and oil crops. The integrity and purity of DNA were detected by agarose gel electrophoresis, Qubit and PCR. The results showed that (1) the plant genomic DNA had high quality and purity, good integrity; (2) one person can handle 2000 samples per day; (3) the obtained DNA samples can be used in gene cloning, transgenic plant detection, CRISPR editing site detection and NGS library construction.