Abstract: We comprehensively evaluated the sustainable development level in China from 2006 to 2016 based on emergy theory. According to the differences in the proportion of primary energy input, all the provinces in China were divided into four groups for inter-provincial comparison to further examine the impacts of primary energy input on the sustainable development. The results showed that under the high economic development, the continuous increase in the primary energy input rate enhanced the environmental load rate of Chinese eco-economic system from 2.78 to 3.13. Meanwhile, the increases in imports led to a decline in emergy yield rate and a decline in emergy sustainable index to 5.40. Results of inter-provincial comparison showed that the trend of emergy per area was generally consistent with the change in the primary energy input rate. Currently, economic development in most provinces was dependent on energy consumption. Among them, sustainable development in cities with dual characteristics of highly developed economics and significant environmental pressures was not optimistic, including Beijing and Shanghai. Provinces in southern China with lower energy input and higher emergy yield were stronger in sustainable development, with Jiangsu as the most representative province. Consequently, improving the efficiency of energy utilization in inland provinces, adjusting the mode of economic development and appropriately slowing down the intensity of economic development could fully alleviate the contradiction between economic growth and environmental protection, and thus steadily achieve sustainable development of ecology and economy.