As agriculture is increasingly challenged by constraints of resources, environment and population emerging from its modern development, it is imperative to explore a kind of sustainable agriculture such as ecological agricultural yards that could accommodate economic, social and ecological needs within an already stressed natural resource basement. To balance the relationships among ecological protection, economic increasing and agricultural development, the establishment of eco-agricultural yards is an effective measure in Three Gorges Reservoir Area. Based on agricultural non-point source pollution zones, this paper dealt with the construction modes and countermeasures of the eco-agriculture yards in Three Gorges Reservoir Area of Chongqing. The results showed: (1) The Three Gorges Reservoir Area of Chongqing was divided into "one line, three zones and six pillar industries" in the whole. And according to the landform, the eco-agriculture yards were designed for three eco-agriculture districts, including the eco-agriculture district in low altitude hilly area, the eco-agriculture district in middle altitude mountain area and the eco-agriculture district in high altitude mountain area. Moreover, the complex agriculture mode with "crop, fruit, vegetables-pigs-biogas-crop, fruit, vegetables+leisure tourism" was suitable for the eco-agricultural development in low altitude hilly area. The eco-agricultural mode with "crop-forest-livestock-biogas-grass" could obtain well effective in middle altitude mountain area. And the eco-agricultural mode with "forest, grass, and livestock" complex mode was available for high altitude mountain area. Considering the development of agricultural industrialization, the ecological plantation, the ecological aquaculture and the ecologically integrated yards were suggested as the construction orientation of eco-agricultural yards in the future in Three Gorges Reservoir Area of Chongqing. (2) On the basis of the existing agricultural non-point source pollution status, Three Gorges Reservoir Area of Chongqing was subdivided into five agricultural non-point source pollution producing zones, involving upstream peripheral hilly area, along the river in upstream hilly area, midstream paralleled ridge-valley area, downstream hilly area, and downstream of the main urban area. Pollution producing regions in upstream peripheral hilly area were suitably dominated by the ecological plantation.More attention should be paid to agricultural non-point source pollution form fertilizers in these regions. Pollution producing regions in downstream hilly area could concentrate on the ecological aquaculture. The eco-agriculture district in low altitude hilly area should regard agricultural non-point source pollution from rural households and runoff as the center of contamination controlling in these regions. And the rest regions were appropriate to the establishment of the ecologically integrated yard. Furthermore, greater monitoring efforts should be put into the pollution producing regions in midstream paralleled ridge-valley area. And, more controlling measures of agricultural non-point source pollution from fertilizers could be applied to eco-agricultural districts in middle altitude mountain area of pollution producing regions along the river in upstream hilly area, while residential areas in middle altitude mountain area were the core for agricultural non-point source pollution controlling in pollution producing regions in downstream of the main urban area. (3) Totally, the eco-agricultural districts in middle altitude mountain area, and the pollution producing regions in midstream paralleled ridge-valley area were the key zones to be constructed, owing to their extensive distribution, favorable natural conditions and more serious agricultural non-point source pollution status. (4) To promote the development of the eco-agricultural yards in Three Gorges Reservoir Area of Chongqing, two aspects were necessary to be considered. That is, the cooperative relationships among the country, government, enterprises and farmers were positively built. And, the high-tech for agricultural production and non-point source pollution controlling measures should be continuously innovated and improved.