This study is an attempt to compare the DNA extraction methods of 7 kinds of extraction: CTAB method, improved CTAB method 1, improved CTAB method 2, benzyl chloride method, lysis method, improved SDS method, and improved urea method so as to isolate high quality genomic DNA from Cordyceps militaris enriching polysaccharides and protein. The results showed that the extraction effect of the third method (improved CTAB method 2) (added low concentration ethanol at purification) was the best. The value of OD260/OD280 was over 1.90, the DNA was amplifiable in the polymerase chain reaction (PCR) and completely digestible with restriction endonucleases HindⅢ.