The urban agglomerations in the Yellow River Basin play a crucial role in preserving the environment and fostering high-quality development in this area. Improving the eco-efficiency of these urban agglomerations has the potential to boost their green economic growth. We approached this from the perspective of urban agglomerations and used the super-SBM model to assess the ecological efficiency of 60 cities across seven urban agglomerations in the Yellow River Basin from 2006 to 2020. Afterward, we analyzed regional differences using the Dagum Gini index and identified the key factors affecting the ecological efficiency of urban agglomerations through the panel quantile model.The results are as follows: ① Eco-efficiency has significantly improved throughout the Yellow River Basin, including all urban agglomerations. The Hu-bao-Eyu urban agglomeration and the Ningxia urban agglomeration along the Yellow River exhibited the highest eco-efficiency levels, while the Central Plains urban agglomeration and the Lanxi urban agglomeration showed the lowest eco-efficiency levels. ② The spatial distribution of eco-efficiency in the Yellow River Basin has shifted from a "clustered distribution in low-value areas, discrete distribution in high-value areas" to a "cross-distribution pattern with small clusters and large dispersion of high-value areas and low-value areas". ③ Overall disparities among the seven major urban agglomerations have decreased. The primary contributors to these differences are disparities between groups and Hypervariable density. ④ Industrial structure, population density, and openness levels constrain the ecological efficiency of urban agglomerations. In contrast, economic development levels and technological progress are positively correlated with ecological efficiency.