Abstract: Quantitative indicators are crucial for analyzing agricultural green development (AGD). Accordingly, the present study aimed to develop a system of indicators to serve for goals of AGD in China based on agriculture and the whole food production-processing-consumption chain. The indicator system included five aspects (society, economy, productivity, resources, and environment) and a total of 53 indicators (27 direct, 14 indirect, and 12 optional). The indicators enabled quantitative analyses of AGD at different scales. Social and economic indicators were calculated using collect statistical data and literature; and then, production, resource, and environmental indicators were calculated using the NUFER (nutrient flows in food chains, environmental, and resources use) model. Criteria for indicator selection, calculation process, and grading standards were also established. Based on the index system, a "top-down" research approach was adopted, and the spatial and temporal characteristics of AGD indicators were quantitatively analyzed at different scales. At the national scale, nitrogen flow in China was quantitatively analyzed, and the overall characteristics, problems, and future optimization strategies for AGD in China were described. From 1980 to 2017, the N use intensity, N production ability, crop protein yield and animal protein yield increased; while the N use efficiency of crop production first decreased and then increased, livestock manure use efficiency decreased and environmental emission cost of resources increased sharply in China. The main reasons for these changes were irrational use of N in crop-livestock production systems, changes in crop and livestock structure, separation of crop production and livestock husbandry, and uneven development of economy and society. At the provincial scale, the characteristics of AGD in the tropical islands of Hainan Province were analyzed. The intensive use of pesticides and N fertilizer was the main limitation of AGD in Hainan. The main impact factors were the high proportion of tropical fruits and vegetables and high density of livestock and poultry breeding At the county scale, both the current status of agricultural development and the resource and environmental costs of Hebei Province were analyzed. High inputs of agricultural chemicals were the main limiting factor for AGD in Hebei. Besides, the disconnection between crop and livestock production was the main limiting factor of AGD. Through benching marking, the spatiotemporal characteristics of green development indicators in the whole dairy industry chain in China was discussed to distinguish the development gap, bottleneck problems and limiting factors. This empirical research indicated that the AGD index system and the NUFER model were useful for quantitatively analyzing the characteristics and costs of AGD at different scales in China.