This paper uses the Super-SBM model with undesirable outputs to calculate provincial green economic efficiency and characterize its dynamic evolution using kernel density estimation. Then, we analyze the overflow effects of innovation output on green economic efficiency by the spatial Dubin model. The green economic efficiency is rising, with the spatial feature of high in the east and south and lower in the west and north. The kernel density distribution curve is moving to the right on the whole, suggesting an improvement in green economy efficiency. The peak value first rises and then decreases, indicating that the growth rate has gone through a process of fast to slow. The double peak state is evident, indicating that the efficiency differences between provinces are increasing. The influence of innovation output on green economic efficiency is significantly positive, with an apparent spillover effect. The spatial spillover effects of economic level, industry structure, environmental regulation, openness, and government support are also significant.