This paper focuses on the total factor water resources utilization efficiency (WRUE) as the research object, employing the Stochastic Frontier Analysis (SFA) model based on the transcendental logarithmic production function to measure the WRUE of nine provinces in the Yellow River Basin of China from 2012 to 2021, obtains WRUE values for each province. And then, we perform a regression analysis of influencing factors using the Tobit model. The results indicate that: (1) The average value of WRUE of nine provinces in the Yellow River Basin is 0.541, which deviates greatly from the fully effective frontier of SFA, with an overall downward trend during the study period. (2) There is a significant polarization of WRUE among the provinces. Inner Mongolia exhibits the highest WRUE at 0.978, close to the SFA efficient frontier, while Ningxia has the lowest WRUE at only 0.314; the remaining provinces display efficiency values between 0.4 and 0.6. (3) Among the influencing factors affecting the WRUE, the value added of the primary industry, per capita disposable income, and the number of reservoirs have a significant positive impact on the WRUE. In contrast, the value added of the secondary industry, local financial environmental protection expenditures, comprehensive water supply production capacity, and per capita daily water consumption negatively affect the WRUE.