Cotton is one of the major honey-source plants. There are mostly genetically modified cotton has been planted in China, in recent years. It raises a concern in consumer wether there are any genetically modified organism in honey. In this research, we used phosphate buffered saline (PBS) to separate high amount of polysaccharide from honey, and improved the concentration of NaCl in extraction buffer to remove the residual polysaccharide, average DNA yield is 486 ng/mL, the ratio of OD260/OD280 is 2.01, and the extracted DNA can meet the requirements of follow-up qualitative PCR testing. The foreign DNA from genetically modified cotton source honey has been detected by PCR. This research would be helpful to improve regulations on genetically modified foods labeling, supervise genetically modified food, reduce trade friction, and protect consumer rights.