Abstract: The construction of Chinese modern agriculture to realize the sustainable development has achieved good results since 80's of the 20 Century, especially, since the beginning of 21 Century, the research and application in eco- agriculture and circular agriculture have been developed rapidly, the connotation and application modes of eco- agriculture is rich constantly, up to now, the connotation of the both show overlapping phenomenon, so, stagger and unclear for eco-agriculture and circular agriculture appear in the design and application areas. Based on research achievements and the development trend of China's ecoagriculture and circular agriculture, the concept of recycling eco-agriculture and design disciplines, it is the basis of agricultural system design, has been put forward by system analysis method and the comparative study; the macroscopic design on a regional scale of recycling eco-agriculture based on industry chains has been formed, it can improve the adaptability of system design, benefiting the design at different levels for the first industry, second industry and third industry of design, and ensure agricultural system development with the adjustment of industrial structure and optimize; The main contents of the regional agricultural system design has been put forward, the method and content of the first industry design been got, including crop farming internal design, husbandry internal design and the first industrial composite design, and the second industrial design, the third industrial design, technical design and policy design is proposed, the results of research provide reference for the development of China’s modern agriculture.