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Abstract: China is now in the process of rapid urbanization. City׳s operating efficiency was directly determined by the scale and efficiency of energy consumption and flow. The pattern, scale and efficiency of urban carbon flow are not only important indicators that reflect urban efficiency and sustainable development, but also important references in the formulating low-carbon and sustainable energy polices for cities. Through establishing a theoretical framework and calculation method, this paper studied the carbon flows of Nanjing urban system in three different levels. It shows that urban production and transportation system, urban living system, rural production system and rural living systems are the major part of urban system in the carbon flow. The carbon flows between Nanjing and the external system, was much higher than the carbon flows among different internal subsystems. If the embodied carbon is taken into account, carbon flow from the urban to rural system of Nanjing was clearly greater than the flow in the opposite direction. With economic development and the implement of energy-saving and emission reduction policy, the carbon productivity and carbon flow efficiency in Nanjing has improved significantly since 2000. Fossil energy consumption, urbanization, agricultural activities, rural life demands and trade are key factors with major impact on urban carbon flows in Nanjing. Therefore, adjusting industrial structure, urban expansion control, and developing renewable energy are main measures to realize sustainable development of Najing city. Furthermore, the dual urban–rural structure in Nanjing brought large exchanges of products and embodied carbon between urban and rural areas, indicates that urban carbon flow and its efficiency was highly influenced by urban–rural structure, which will further aggravate carbon flow burden of urban systems. [Copyright &y& Elsevier]