Taking capital, manpower, and natural resources as inputs, regional GDP as expected output, and industrial pollution as undesired output, this study measures the ecological efficiency of various regions in China through the Global-Malmquist model. The results show a trend of an initial sharp decline in ecological efficiency followed by a gradual increase in the time dimension, but there is no significant correlation in the spatial dimension. Using the gravity model to quantify the attractiveness of the regions’ capital and human resources for collaborative innovation, it estimates the impact of collaborative innovation on eco-efficiency through the system-Generalized Method of Moments (GMM) model. The results show that technological innovation capital in other regions has a negative “U” relationship with local ecological efficiency, while scientific and technological innovation human resources have a positive “U” relationship. In addition, government financial support in science and technology and the ecological efficiency of the previous period serve as promoting factors of the current local ecological efficiency, while the introduction of foreign technological innovation is likely to inhibit improvements in ecological efficiency. Based on these findings, this study puts forward corresponding policy recommendations for local governments to advance their development agendas alongside their environmental priorities in line with their specific circumstances.