The development of eco-innovation varies across different countries, as does the development of eco-innovation systems. Eco-innovation system is a network system formed by a series of participants through interaction. The purpose of eco-innovation system is to improve the production, diffusion and application of knowledge and technology conducive to coordinating ecological conservation, environmental protection and socio-economic development. To compare and analysis quantitatively the development and sustainability of eco-innovation systems in major advanced countries, as well as to describe and analysis the advantages and disadvantages in these innovation systems more precisely, this paper proposes a two-step model and an overall framework to evaluate eco-innovation systems. Firstly, the study combines function and process assessments to evaluate the development level of eco-innovation system. Secondly, the study focuses on the long-term development of the systems, namely system sustainability. A model evaluating the sustainability from the perspective of capital, which includes knowledge capital, economic capital, human capital and social capital, is exploited. The stock, flow and risk factors of these capitals are considered as well. Based on the theory of innovation system, literature review, and comparison of international research, 30 key indicators are selected, and a complicated indicator system involved two index matrices are construed. Principal component analysis and comprehensive evaluation are used to evaluate the function-process and sustainability of eco-innovation systems in different countries. The results show that France, Germany, South Korea, Spain and Norway exhibit strong performance in terms of eco-innovation system function and system process. The eco-innovation systems of South Korea, Germany, Austria, Norway and Czech Republic have the best sustainable performance. According to the development and sustainability of their eco-innovation systems, the countries can be classified into four groups, and different strategies can be adopted accordingly. South Korea is an eco-innovation leader, and its system has strong performance and sustainability. The system of Spain has high development but weak sustainability, and it is necessary to increase investment in eco-innovation. Turkey has weak performance and weak sustainability, while the two aspects of Netherland are relatively balanced. In addition to increasing capital investment, Turkey should also strengthen the improvement of system functions and the optimization of innovation process. The research not only improves the integrated evaluations of the function and the process of innovation systems, but also makes up for research on sustainability. Moreover, the results provide a scientific basis and data to support the improvement of eco-innovation systems and the introduction of relevant eco-innovation policies in these countries.