The sustainable logic between the Agricultural Heritage System (AHS) and environmental synergy has been significantly changing with China’s urban–rural relationship shift from binary opposition to a stronger network exchange. During the process of transformation, China’s AHS rural areas encounter two major development trends and social realities, i.e., whether to continue conventional characteristic agricultural development or detach from conventional characteristic agricultural resources to achieve industrial transformation. Our aim is to analyze the structure, identity and functional transformation characteristics of AHS rural areas from the urban and rural scale, as well as to build an explanatory framework for transformation mechanisms. A total of 109 counties and five cases of important AHS areas in China are taken as research objects, combining quantitative and qualitative analyses to analyze the transformation of AHS rural areas from two aspects. On the one hand, for changes in single development elements, there are three development elements and corresponding transformation dimensions: (1) Land structure: there is a synergistic change between the increase in urbanization rate and the loss of rural land, with associated changes in space and production structure. (2) Population identity: the rural population loss in high-urbanization-level areas is severe, where farmers are combined or separated from traditional agriculture. (3) Industry function: the trend of non-agricultural development of the industrial economy is obvious, and the traditional functions of agriculture are facing a continuation or a deep transformation. On the other hand, for relations among development elements, combined with a regression analysis and field investigation, we try to explain how the development elements and characteristic elements influence each other while working together on the transformation of AHS rural areas. The transformation depends on the path of the original industrial structure, while the urban–rural income ratio, regional distribution and land urbanization rate all positively stimulate the transformation from agricultural industries to non-agricultural ones. Moreover, the transformation of AHS rural areas is also affected by the characteristic elements of their special agricultural heritage, specifically, whether the heritage is scalable, scarce or socialized, etc., and these special attributes can determine the different development forms of heritage elements in the modern agricultural industrial system.