To understand the sustainable development ability of a regional eco-economic system, this paper constructed a DEAHP model and an evaluation index system by combining the connotations and characteristics of the internal structure of a regional eco-economic system. Furthermore, we evaluated the sustainable development level of both provincial and regional eco-economic systems from 2007 to 2012 in China. The results showed that the degree of the overall order in China increased monotonically and was relatively low. In addition, the results show that, for the three regional eco-economic systems in China, the eastern region differs remarkably from the western region but two neighbouring regions are relatively closer. The results are very much the same at the provincial level. Also, at the provincial level, the sustainable development ability of a provincial eco-economic system is positively correlative with the development of local economy. This paper presents a feasible research framework, which uses a DEAHP model to evaluate a regional eco-economic system and provides theoretical and practical guidance for the sustainable development of regional eco-economic system in China.