The author of this paper thought that agricultural non-point pollution was the most important source of water pollution based on the analysis of the present situation of the agricultural non-point pollution in China and its reasons. In order to improve the water environment, the meaning and content of the eco-agricultural industrial chain was introduced. Based on this conception, the eco-agricultural industrial chain, integrating a whole circular system with different sessions of crop farming, breeding, agricultural products processing and living, was innovatively put forward to control the agricultural non-point pollution and protect the water environment systematically for the first time in this paper. Concretely, in the principle of source harmlessness, process resource utilization, end ecological treatment and controlling in large-scale, several important techniques were included as manufacturing of ecotypic feeds, ecological breeding with zero discharge of pollution, production of biological humic acid fertilizer with fermentation bed padding, eco-planting with controlling of nutrients release and programming and construction of eco-agricultural park. In combined application of these techniques, the eco-agricultural industrial chain technology was proved to be an efficient method to achieve both the well control of agricultural non-point pollution and effective improvement of the water quality.