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Cities are the spatial carriers of ecological protection and high-quality development in the Yellow River Basin’s nine provinces（regions). With the help of eco-efficiency, we can reveal the coordinated development of ecology and economy. In the existing studies, urban eco-efficiency is usually measured under the same external conditions, but little consideration is given to the differences of cities. By constructing a three-stage super-efficiency SBM model after excluding external environmental factors, this paper calculated the ecological efficiency of 57 cities in nine provinces（regions） of the Yellow River Basin from 2010 to 2019, and further analyzed the spatial-temporal differentiation characteristics of urban ecological efficiency in nine provinces（regions） of the Yellow River. The results show that compared with the traditional super-efficiency SBM model, the three-stage super-efficiency SBM model is more reasonable. After excluding the influence of environmental variables such as income level, industrial structure, environmental policy and foreign direct investment, the urban eco-efficiency of nine provinces（regions） in the Yellow River Basin decreases slightly. In terms of time evolution characteristics, the eco-efficiency value of most cities in the nine provinces（regions） of the Yellow River Basin shows a fluctuating downward trend, and the eco-efficiency of cities in the upper reaches decreases significantly. In terms of spatial distribution characteristics, most cities in the nine provinces（regions） of the Yellow River Basin are concentrated in low eco-efficiency areas, showing an alternating spatial distribution trend of “low-high-low-high” from west to east. [ABSTRACT FROM AUTHOR]