摘要:Eco-innovation is the main driver of realizing the coordinated development of resource, environmental and economic systems. This paper measures regional eco-innovation efficiency (<i>EIE</i>) by using the Super-Slack Based Measure (SBM) model with undesirable outputs and distinguishes different agglomeration patterns based on Chinese data of 21 manufacturing sub-industries of 30 provinces. In particular, from the perspective of the dynamic evolution of manufacturing agglomeration, the nonlinear effects of specialized and diversified agglomeration on <i>EIE</i> are investigated based on panel threshold regression models. The results indicate that China’s <i>EIE</i> shows a U-shaped changing trend. The impacts of specialized and diversified agglomeration on <i>EIE</i> are nonlinear and have significant three-threshold effects. There exist a U-shaped relationship between specialized agglomeration and <i>EIE</i>, and an S-shaped relationship between diversified agglomeration and <i>EIE</i>. In terms of eco-innovation, the development of diversified agglomeration is superior to that of specialized agglomeration. Overall, there is still much room for more than 70% of provinces in China to increase their <i>EIE</i> by optimizing the layout of manufacturing specialized and diversified agglomeration. To improve the <i>EIE</i> and achieve sustainable economic growth, differentiated agglomeration policies should be formulated in various stages and regions. In addition, the driving mechanism of eco-innovation should be strengthened.