In order to understand whether the debate on GMF have an influence on the public’s risk perception and find its causes comprehensively and objectively.The Logistic model is established and analysized by the data surveyed randomly in 6cities in this paper.The result shows that the public’c risk perception of GMF concentrates on the health risk and environment risk,the debate on the GMF has an obvious influence on the public’c risk perception of GMF.Accoring to the root of the debate,both the public’s understanding on the GMF debate and the knowledge about GMF,the education level have an significant influence on their risk perception of GMF,the uncertainty of GMF and the sensitivity on the food affects the public’s risk perception,the percentage of the lacking of communication between the scientist and the public only have influence on the human health remarkablely.Based on that,suggestions that strengthening publication power for GMF,building the interaction platform between scientists and the public,setting up the GMF information disclosing system have been proposed in this paper.