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Research on carbon cycling has attracted attention from both scientists and policy-makers.Based on material flow analysis,this study systematically budgets the carbon inputs,outputs and balance from 1980 to 2013 for China’s agro-ecosystem and its sub-systems,including agricultural land use,livestock breeding and rural life.The results show that from 1980 to 2013,both the carbon input and output were growing gradually,with the carbon input doubling from 1.6 Pg C/year in 1980 to 3.4 Pg C/year in 2013,while carbon output grew from 2.2 Pg C/year in 1980 to 3.8 Pg C/year in 2013.From 1980 to 2013,the crop production system in China has remained a carbon source,and the agricultural land uses were also almost all carbon sources instead of carbon sinks.As soil carbon stock plays a very important role in deciding the function of China’s agro-ecosystem as a carbon sink or source,practices that can promote carbon storage and sequestration will be an essential component of low carbon agriculture development in China.