As a major energy producer and consumer, China has witnessed rapid growth in carbon emissions, which are closely linked to changes in regional climate and the environment. Water, energy, and food (W-E-F) are the three most critical components of human production and daily life, and achieving the coordinated development of these three resources and connecting them with climate change through the carbon emissions generated during their utilization processes has become a key issue for realizing regional ecological sustainable development. This study constructs a dynamic two-stage network slack-based measure-data envelopment analysis (SBM-DEA) model, which integrates the water–energy–food (W-E-F) system with the climate change process to evaluate China’s comprehensive ecological efficiency from 2011 to 2022, and adopts the Dagum Gini coefficient decomposition, kernel density estimation, hierarchical clustering, and geographical detector model to analyze provincial panel data, thereby assessing efficiency patterns, regional differences, and driving mechanisms. The novelty and contributions of this study can be summarized in three aspects. First, it establishes a unified framework that incorporates the W-E-F nexus and climate change into a dynamic network SBM-DEA model, enabling a more systematic assessment of ecological efficiency. Second, it uncovers that interregional overlap effects and policy-driven factors are the dominant sources of spatial and temporal disparities in ecological efficiency. Third, it further quantifies the interactive effects among key driving factors using Geodetector, thus offering practical insights for regional coordination and policy design. The results show that China’s national ecological efficiency is at a medium level. Southern China has consistently maintained a leading position, while provinces in northwest and southwest China have remained relatively backward; the efficiency of the water–energy–food integration stage is relatively high, whereas the efficiency of the climate change stage is medium and exhibits significant temporal fluctuations. Interregional differences are the main source of efficiency gaps; ecological quality, environmental protection efforts, and population size are identified as the primary driving factors, and their interaction effects have intensified spatial heterogeneity. In addition, sub-indicator analysis reveals that the efficiency related to total wastewater, air pollutant emissions, and agricultural pollution shows good synergy, while the efficiency associated with sudden environmental change events is highly volatile and has weak correlations with other undesirable outputs. These findings deepen the understanding of the water–energy–food-climate system and provide policy implications for strengthening ecological governance and regional coordination.