The rational and efficient use of urban land resources and ecological environment management can strengthen the ecological protection and high-quality development process in the Yellow River Basin. Therefore, it is crucial to effectively measure urban land use efficiency and eco-efficiency. Based on Stochastic Frontier Analysis (SFA) model, this study measures the Land Use Efficiency (LUE), Ecological Performance Index (EPI) and Ecological Efficiency (EE) of 59 cities in 7 urban agglomerations in the Yellow River Basin and analyzes their spatial and temporal variation patterns from 2005 to 2018. Then, this study conducts the spatial autocorrelation analysis of LUE and EE, and further explores the relationship between LUE and EE. The results of this study show that the mean land use efficiency increases by 4.43% after the addition of ecological variables when comparing the test results of the unconstrained model with those of the constrained model. The mean value of land use efficiency of the urban agglomerations in the Yellow River Basin is 0.89, and most cities show an increasing trend of land use efficiency, with the spatial distribution characteristic of low in the west and high in the east. The percentage of cities with ecological performance index greater than 0 is more than 90%, indicating that the addition of ecological variables contributes to the improvement of land use efficiency of most cities in the Yellow River Basin. The annual mean value of ecological efficiency of urban agglomerations in the Yellow River Basin is 0.62, which shows a spatial distribution pattern of high in the west and low in the east, and significantly positively spatial aggregation pattern characteristic. With further analysis, we find that ecological efficiency and land use efficiency change in a U-shaped relationship, indicating that land use efficiency shows a trend of first decreasing and then increasing with the increasing ecological efficiency. This study reveals the relationship among urban land use, ecological benefits and social-economic effects in the urban agglomerations of the Yellow River Basin, which can provide a reference for the development of new urbanization, efficient use of land resources, ecological protection and high-quality development in the Yellow River Basin. Based on the empirical analysis results, we suggest that the Yellow River Basin is supposed to improve the intensity of resource utilization, optimize the allocation of various resources for cities in the basin, deepen cross-regional exchanges and cooperation among different urban agglomerations and cities, focus on the improvement of urban ecological efficiency, and build a high-quality development pattern in the future.