Against the background of a high-quality development philosophy, the realization of the coordinated development of the economy, environment, and resources is particularly important. This study adopts the super-efficiency slacks-based measure (SBM) model to evaluate the eco-efficiency of 208 cities in 19 urban agglomerations in China from 2006 to 2020, and the kernel density estimation and spatial econometric specifications are combined to reveal the spatial-temporal evolution. Finally, Tobit regression is used to analyze the driving factors of the eco-efficiency of urban agglomerations in China. The main results can be summarized as follows: (1) The eco-efficiency of Chinese urban agglomerations is generally low, and the differences in eco-efficiency between urban agglomerations are obvious, with different trends of change. (2) In terms of the time series, the sample period shows a "steadily rising" trend followed by a "fluctuating downward" trend. From the results of the kernel density estimation, the internal difference in the overall eco-efficiency of urban agglomerations shows the trend of a small decline followed by a gradual increase. (3) From the spatial point of view, the eco-efficiency of urban agglomerations decreased from the coast to the inland areas, and there was a "cluster effect". The overall eco-efficiency of urban agglomerations shows a trend of spatial aggregation. (4) From the perspective of influencing factors, fiscal expenditure, opening-up level, and population density have a significant negative correlation with the eco-efficiency of urban agglomerations, while science and technology investment, industrial structure, and urbanization level have a significant positive correlation with the eco-efficiency of urban agglomerations. The research in this paper provides guidance for the coordinated development of urban agglomerations and the formulation of environmental policies.