Eco-efficiency is an instrument for sustainability analysis, which takes into account both economic and environmental performance. This study aims to develop appropriate indicators for the economic and environmental dimensions of the eco-efficiency analysis, and the method for aggregating them, to illustrate possibilities for measuring regional eco-efficiency. A starting point is to produce indicators for the environmental and economic dimensions of regional development and to use them for measuring regional eco-efficiency. Based on material flow analysis (MFA), basic and broader definitions were applied for regional eco-efficiency analysis. In the physical economy, we input material and energy, and produce products (or value), while the wastes and emissions (or for other undesirable outputs) are unavoidable. Thus, there are two essential classes of environmental impacts: resources consumption and pollution discharge. Waste water, waste gas, and solid waste and carbon dioxide were chosen as pollution discharge indicators and direct material input and total material requirement were chosen as resource consumption indicators for narrow and broad regional eco-efficiency analysis, respectively. On the other hand, the economic indicator used was the gross domestic product (GDP) of research site. Subsequently, two data envelopment analysis models were applied to aggregate eco-efficiency indicators, by taking various undesirable outputs (pollution discharge) as inputs. Using the real data of Jiangsu Provinces (from 1990 to 2005), an empirical study was employed to illustrate the changes of regional eco-efficiency. The results showed that the eco-efficiency of Jiangsu Province increased from 1990 to 2005, and the years 2003, 2004 and 2005 were relatively eco-efficient compared to other years. However, Total Material Input (TMI), Total Material Requirement (TMR) and pollution discharge also increased simultaneously. Thus, economic development and environmental impact represented weak de-linking.