Improving eco-efficiency is an important way to promote ecological civilization and green development. Taking the Central Plains Urban Agglomeration as the research object, this paper firstly used Super-SBM model to calculate the eco-efficiency of 29 cities from 2003 to 2016, used GIS technology to depict the spatio-temporal evolution and spatial correlation characteristics of eco-efficiency, then analyzed the influencing factors of eco-efficiency by using spatial lag model. The results showed that: (1) The eco-efficiency of the Central Plains Urban Agglomeration presented an overall stepped trend from 2003 to 2016. There were differences among regions with a pattern of high in the north and south but low in the middle. (2) The eco-efficiency of the Central Plains Urban Agglomeration showed the significantly positive spatial autocorrelation and the degree of spatial agglomeration gradually increased. The cold spots changed dynamically in the northwest and the southeastern parts formed stable hot spots. (3) There was a significant spillover effect of eco-efficiency, a significantly positive effect on the level of economic development and the level of openness, while a significantly negative effect on the level of science and technology.