In response to the 14th National Five-year Plan of China and to better explore new strategies for promoting regional coordinated green development, the eco-efficiency values of Chengdu-Chongqing Economic Circle and the corresponding temporal analysis from 2004 to 2018 were assessed in this paper using the super-SBM model and Markov chain. Meanwhile, the spatial analysis of eco-efficiency was conducted by a geographically weighted regression model. Although eco-efficiency has risen at an increasing rate, the economic development of Chengdu-Chongqing Economic Circle was still ecologically ineffective. This means there is an urgent need to improve the efficiency of resource utilization and promote technological innovation. During the study period, the evolution of the eco-efficiency presented as a “π” shape, and was accompanied by the phenomenon of “club convergence”. There was also a strong tendency for eco-efficiency to maintain the original status quo, which indicates that it lacked sufficient momentum for improvement, so it was difficult to achieve a leapfrog transfer. Spatially, the eco-efficiency was distributed from northwest to southeast in a high-low-high manner. The spatial-temporal differences of eco-efficiency narrowed but the effect of agglomeration was relatively weak and there was a polarization trend. Further investigation suggests that the differences in the development level of urbanization, opening, technology, environmental regulation and advancement of industrial structure led to the spatial differences of eco-efficiency. Each city in the Economic Circle should make every effort to improve eco-efficiency accordingly, and thus to promote the green development of the whole region, so as to lay a foundation for driving the green and coordinated development of the central and western regions.