<p>The green partnership of the water-energy-food-ecology (WEFE) system is essential to advance regional eco-friendly development. Firstly, based on the input–output theory, a multidimensional green efficiency measurement indicator system for the WEFE system was constructed. Secondly, a measurement model integrating a deep learning method and the slack-based measure directional distance function method was developed. Finally, with the Yellow River Basin (YRB) of China as the research area, the spatiotemporal differentiation characteristics of the green efficiency of the WEFE system from 2011 to 2022 were analyzed. The research results indicate that: (1) In terms of temporal evolution, the green efficiency of the WEFE system in the YRB showed a significant upward trend. This improvement happened in three stages: rapid growth in 2011–2015; steady development in 2015–2019; and fluctuating growth in 2019–2022. (2) Spatially, green efficiency was lower in the upstream provinces and higher in the midstream and downstream provinces. (3) Regarding the spatial correlation, green efficiency had significant positive spatial autocorrelation after 2013, with the agglomeration effect continuously strengthening and peaking in 2019. Locally, spatial clustering was manifested as “high-low” clusters in the upstream and “high-high” clusters in the midstream area. This study enhances understanding of WEFE system adaptation in the YRB, informing regional multi-resource collaborative management.</p>