The idea of sustainable development has been gradually established since 1970s. A variety of theories and indicators have been proposed under the guidance of the concept of sustainable development, like industrial ecology, eco-efficiency, eco-design, the revolution of ‘X’. Among them, eco-efficiency has been recognized as a route to promote a transformation towards sustainability. The essence of ‘efficiency’ is the ratio of system’s outputs and inputs. While the prefix of ‘eco-efficiency’ is ‘eco’, which stands for both ‘economic’ and ‘ecological’ dimensions and can be used for systems like product, technology, enterprise, organization, country. Eco-efficiency is a useful tool for quantitative analysis of the system sustainability that it is easy to understand and communicate, open and expansibility. Eco-efficiency will provide good support for measuring, analysis and research work in sustainable development. Under the guidance of social-economic-natural complex ecosystem, this article mainly takes researches of measuring method and assessment model in industrial systems from different scale. First, the relationship between regional industrial systems based on industry linkages had been studied. Multiple regional input-output model describes all the goods within industry chains, so it can tracking the environment impact which attached to commercial trades among regions. In our research, under the assumption that the industry sectors are the same both in and abroad China, a modified multiple regional input-output model was illustrated to study the direct and indirect energy eco-efficiency. The results show that: the inter-regional transfer of energy and environmental impacts can be accounted and located according to the indirect energy eco-efficiency analysis in 8 regions and 17 sectors; the friendly relationship between regions can be judged. All of the accountings are useful for macro decision-making. Then, based on the consideration of treating environmental impacts as undesirable outputs, an eco-efficiency assessment data envelopment analysis model and a super data envelopment analysis model was established. When making a case study of Chinese provincial capital cities, the results show that: more than half of the cities were relatively eco-efficient, the relatively in-efficient cities mainly located in the southwest and northwest of China which is the developing areas. According to the benchmark and sequence analysis, Haikou, Fuzhou, Beijing was the top three while Yinchuan, Lanzhou, Guiyang was the last three. When make a further exploration of the variables of the input indicators, there exist a large space for the reduction of the total input indicators. What’s more, an eco-efficiency framework for city time series accounting was established when coalescing the ecological services and eco-efficiency together. When taking Changzhou as a case study, the 25 years (1986-2011) eco-efficiency was measured, the results show that: the eco-efficiency of Changzhou had been promoted a lot, and the environmental efficiency played a dominant role in accordance with the contribute rate; when making a further explore of the resource efficiency, we have found that the energy efficiency increase slightly and had a sharp drop in 2011, all of these demonstrated that the energy efficiency was the key elements to Changzhou sustainable development. Finally, the eco-efficiency between the National Economic and Technological Development Zone (NETDZ) and the city area which they located had been calculated, the interaction between the two subjects had been discussed, and a land conjugated ecological management based on the ecological service has been proposed. It will provide a new model for land management by the innovation of management strategy, technology and engineering. According to our research, an eco-efficiency framework and indicators had been established and make case studies in different industry system. The identical characteristic