Genetically modified (GM) crops have been widely planted worldwide and contribute greatly to food security and environment sustainability. Although China is one of the major countries planting GM crops, recent progress is slow. In the past 20 years, Chinese government has maintained a positive attitude towards the GM organisms and provided the most supportive policies on agricultural biotechnology researches, however, public opinions have becoming perceivably against GMOs with presumptive concerns on human health, economic benefits and environment. Poor communications between scientists and the public, weak GMO governance among different departments, hesitation to advanced technology, variable and non-evidence based voices from media, as well as global anti-GMO organizations, are among the important aspects in this conflict. Possible solutions to solve the conflict are discussed.