With the further implementation of the rural revitalization strategy, China's rural areas have entered a critical stage with priority development. It is of great significance for the implementation of the strategy of agricultural and rural priority development to scientifically understand the law of urban and rural element allocation and guarantee approaches under the guidance of rural priority development. This paper is based on the regional system theory of human-land relationship and the developmental logic with "Element-Structure-Function". The scientific connotation for urban-rural relationship and element priority guarantee under the guidance of rural priority development is analyzed in this study. This paper sorts out the evolution characteristics of urban-rural relationship and element flow in China from three aspects, namely, the evolution of urban-rural relationship affecting element flow, the division of element flow stages and the overall characteristics of element flow. In addition, it builds a regulatory framework of priority guarantee of rural element from the aspects of element integration, spatial integration and mechanism coordination. The results show that rural priority development is an evolution process based on rural elements, optimizing rural structure and realizing rural functions. The development of relations between urban and rural areas in China has initially gone through the preferential development in urban areas, the coordinated development between urban and rural areas as well as the integration development for urban and rural areas. What's more, the rural element allocation generally encounters such problems as less types for flow elements, poor element outflow and inflow, as well as unsound element flow. It aggravates the imbalance of the type, direction, scale and efficiency of element flow between urban and rural areas in urgent need of external intervention and regulation. At the current stage, there is an urgent need to expand the types of mobile elements in rural areas, to enhance their mobility, to strengthen the weak links in infrastructure, to dredge the stock of elements flowing into the city, to expand the channel of elements flowing into the countryside as well as to expand the "gray space" in urban and rural areas. It aims to expand the rural flow element types, to enhance its flow property, to improve urban elements into the country and to make a long-term development environment. In the end, the priority allocation targets of rural elements should be achieved, including rural elements flow, urban elements flow and scarce elements, so as to ensure the priority of agricultural and rural development.