By using data envelopment analysis and Malmquist index, the water resources utilization efficiency of 68 administrative units in the Yellow River Basin was calculated. The results show that in 2017, there were 26 prefecture level administrative units with DEA efficiency and 42 prefecture level administrative units without DEA efficiency in the Yellow River Basin. By calculating the input redundancy of 42 administrative units without DEA efficiency, it is found that there are 27 due to low scale efficiency and 15 due to low technical efficiency. From 2009 to 2017, the utilization efficiency of water resources in the Yellow River Basin presents the characteristics of first rising, then falling, and big fluctuation. The overall utilization efficiency of water resources has been improved, and the technical level is the key factor. From the perspective of basin, the comprehensive average value of TFP index of water resources in the Yellow River Basin from 2009 to 2017 is 0. 957. Among them, the downstream has the highest water resources utilization efficiency, with TFP index of 0. 977, and the upper and middle reaches are next, with TFP index of 0. 958 and 0. 948, respectively.