The rapid growth of grain yield in China accelerates a discussion on whether the grain system in China is sustainable.  To answer the question, a comprehensive assessment from economic and environmental points is necessary.  This study jointly used economic analysis (ECA), emergy evaluation (EME) and carbon footprint (CF) to analyze the environmental and economic sustainability of the grain production system in China based on the national statistical data during 2000–2015.  Results showed that the costs of maize, wheat, rice and soybean had increased by 252−346% from 2000 to 2015, causing the lower profit of grain system in recent years.  The situation resulted in a serious problem on economic sustainability of grain system in China.  Meanwhile, the emergy sustainability index (ESI) of maize, wheat, rice and soybean systems were increasing during 2000–2015, and the CF on unit yield of the crops had been reduced by 10−30% in the study period.  The results reflected the improved environmental sustainability of grain system in China during 2000–2015.  Nevertheless, the emergy flow of industrial inputs for the crops were increased by 4−22% in the study period, and the CF from the inputs presented a growth rate of 16−23% as well during the same period.  The results implied that the grain system in China was relying more on fossil-based inputs.  Finally, according to the key points of cost, emergy and CF, we suggest that improving labor efficiency, advanced agricultural practices and optimizing cropping pattern will be effective ways to further improve the economic and environmental sustainability of grain system in China.