The flexible management of engineering agriculture is a kind of management idea that promotes to put the engineering management mode into agricultural production. Based on the analysis of characteristics of agriculture and combined the idea of industrial production, the article explained the connotation of the flexible of engineering agriculture, analyzed its three dimensions consist of productivity, producer and relation of production. At last the paper introduced the innovative application in productivity of this idea, put forward the concept of decision making quality of farmers and explained the organization policies of agriculture of our country.