With the rapid development of the industrialization of transgenic crops of the whole world,China’s industrial system of modern agriculture continues to highlight the strategic position of genetically modified seed market.However,when the commercial cultivation of genetically modified rice is very likely to be carried out,the regulations of genetically modified seed market as well as the cognition of farmers and so on are still faced with many problems.On the basis of the information obtained from the investigation of farmers in three regions,namely Shandong,Hubei and Chongqing,with a better comprehension of Chinese farmers’ cognition status towards the genetically modified seed market and the current difficulties,counter measures to develop harmoniously the genetically modified seed market were presented in the aspect of regulation perfection.