Lucid waters and lush mountains are invaluable assets. Resource-saving and environmentally friendly industrial structures, production, and living modes are pursued continuously for sustainable ecological development. According to the Second National Pollution-Source Survey, agricultural non-point pollution is still the most important source of the current water pollution. In order to improve the water environment and control the pollution, 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, animal breeding, agricultural product processing, and rural 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. The sustainable development was realized at a large scale from the reduction and harmlessness at the source, resource utilization in the process, and ecological restoration in the end. Core techniques were innovated based on the integration of agricultural industries to achieve the high-quality and green development of agriculture. The system included ecological breeding technologies, ecological cultivation technologies, as well as rural sewage treatment and recycling technologies, in the principle of reduce, reuse, and resource. Based on this, the agricultural production changed from the traditional mode of “resources–products–wastes” to the circulation pattern of “resources–products–renewable resources–products”. Thus, the final aim could be achieved to realize the material’s multilevel use and energy conversion in the system. The eco-agricultural industrial chain technology was proven to be efficient to achieve both the good control of agricultural non-point pollution and an effective improvement in the water quality.