Improving water use efficiency is the key measure to realize the sustainable development of water resources. It is of great significance to explore the spatial pattern and dynamic change of water use efficiency in order to promote the ecological protection and high-quality development of the Yellow River Basin. In this study, we built a global Minimum Distance to Strong Efficient Frontier (MinDS model) based on unexpected output to accurately measure the water use efficiency of the Yellow River Basin from 2000 to 2017. The spatial pattern of water use efficiency of the Yellow River Basin was comprehensively depicted from the perspective of national, regional, and intraregional comparisons. The change of distribution dynamics of water use efficiency was investigated by an extended distribution dynamic model. The results show that the water use efficiency of the Yellow River Basin is higher than the average level in China. The water use efficiency of the lower reaches is higher than that of the upper reaches. A spatial pattern of “high in the east and low in the west” is very clear. The polarization of water use efficiency in the Yellow River Basin is obvious in some years. Spatial factors can significantly affect the regional distribution of water use efficiency. The interaction of water use efficiency in adjacent areas leads to the gradual narrowing of water use efficiency gap in the Yellow River Basin in the long term. And water use efficiency converges to the middle level.