Abstract: Regional Eco-innovation covers the level of regional economic development, innovation capabilities and environmental sustainability. It is a combination of innovation-driven development strategy and ecological civilization construction. This paper divides the Eco-innovation process into technology research and development stage and achievement transformation stage, and incorporates waste recycling, energy consumption and undesired output into the innovation process, and constructs a closed-loop network structure of the Eco-innovation process. On the above basis, combined Super-efficiency model and SBM model, proposed an improved network DEA model that considers waste recycling and undesired output, which is used to measure the overall efficiency of regional Eco-innovation and the efficiency of each sub-stage, further establishes a measurement model of Eco-innovation scale efficiency to explore the scale efficiency of each decision-making unit. Finally collect the relevant panel data of China's regional innovation to conduct an empirical analysis, and the results show that the proposed method is effective and feasible. This paper expands the research on the Eco-innovation efficiency base on the network DEA structure, from the perspective of closed-loop Eco-innovation of waste recycling, it provides a certain theoretical reference and practical enlightenment for the optimal allocation of regional innovation system resources.