Achieving synergistic development of efficient urban land use and the natural environment is crucial in promoting green urbanization. The assessment of land use eco-efficiency (LUEE) and its temporal–spatial changes provides an effective means of quantifying the relationship between the urban ecological environment and land use. Targeting 55 selected cities in the Yellow River Basin (YRB), in this study, we utilize the Super-EBM method to gauge the LUEE. We explore the temporal patterns and the spatial convergence of LUEE utilizing kernel density estimation and spatial econometric methods. Considering the resource and environmental costs of land use, we assumed the industrial pollutant emissions generated during urban land use as the undesired outputs and designed a framework for measuring the level of LUEE under double constraints, which theoretically revealed the formation process and spatial convergence mechanism of LUEE. The results show the following: (1) Throughout the sample period, the LUEE of the YRB urban agglomeration decreased from 0.158 in 2009 to 0.094 in 2020, indicating a decreasing spatial disparity in LUEE over time. Notably, the Lanxi urban cluster exhibited the largest gap in LUEE, whereas the Guanzhong Plain urban agglomeration displayed the smallest gap. The hyper-variable density exceeded the inter-group gap as the main factor leading to the difference in LUEE. (2) Although the LUEE of urban agglomerations has increased, there still exists a noticeable polarization phenomenon. (3) The LUEE of YRB demonstrates a pattern of conditional convergence and exerts a significant spatial spillover effect. Over time, the LUEE of YRB will tend towards an individual steady state. The findings have implications for strengthening linkage and synergy among cities in YRB, promoting factor integration across administrative regions, and formulating heterogeneous policies.