Ecological well-being performance (EWP) is a key indicator of sustainable development and has garnered significant research attention. This study measures the overall and stage-by-stage efficiency of the urban agglomerations in the Yellow River Basin based on the ends–means framework of steady-state economics. This study then delves into the spatiotemporal transfer characteristics of EWP through Moran’s I, and spatial Markov chains. Additionally, this research investigates the factors influencing EWP using a random forest model. The findings indicate a notable enhancement in EWP in the urban agglomerations in the YRB from 2006 to 2021, showing clear spatial agglomeration patterns. The shift in EWP types displays a “path dependence” effect, with distinct evolutionary paths influenced by spatial lag effects. Ecological input emerges as a key internal driver of EWP, while urbanization and technological advancements are highlighted as significant external factors. Industrial agglomeration and industrial structure also contribute to improving EWP. The findings of this study help to clarify the spatial and temporal characteristics of ecological welfare performance and its driving mechanisms in the urban agglomerations of the Yellow River Basin. This is conducive to the achievement of high-quality urban transformation and regional green development, and it provides a reference for the construction of an ecological civilization.