By constructing an ecological efficiency evaluation system that reflects the overall environmental quality and economic development status, and applying the super efficiency SBM model, the ecological efficiency of 182 cities in the Yangtze and Yellow River basins was calculated and evaluated.Combining the spatial Durbin model, the main influencing factors and spatial spillover effects of ecological efficiency in two basins was discussed.The results show that during the study period, the ecological efficiency of the Yangtze and Yellow River basins showed a fluctuating growth trend, and there were significant regional differences in ecological efficiency in the two basins.Furthermore, it was found that industrial structure, economic development level, and scientific and educational intensity have significant spatial spillover effects on the ecological efficiency of the two basins.Finally, countermeasures and suggestions to promote technological innovation, optimize resource allocation, and optimize industrial structure were proposed, in order to assist in the coordinated development of ecological efficiency in the two basins.