Eco-efficiency is an important approach for economic sustainability analysis indicating how efficient the economic activity is, considering environmental risk analysis simultaneously. Traditional DEA framework neglect the undesirable output during the process of production, in industrial society lots of harmful by-products are made at the same time, which lead to serious environmental pollution and risk. In this paper we adopt a non-radial undesirable output DEA model to measures the eco-efficiency of each province in China. The conclusion is that economically developed area eastern part has the highest eco-efficiency, while less developed area western part has the worst eco-efficiency that may cause great environment risk. The western area is in a dilemma situation facing the poor economic and bad environmental condition. We suggest that the western area can purchase waste discharge right from more developed area to settle this problem provisionally.