Herein, we investigated the relationship between water, food, and energy (W–E–F) in different regions of China to provide suggestions for sustainable and stable regional development of these resources. Based on the system theory, we constructed three relevant subsystems and analyzed the action mechanism between them. Furthermore, we constructed a network based on the super-efficiency data envelopment analysis model for a W–E–F input–output index system. This model was applied to 30 areas in China from the year 2005 to 2015 for measuring W–E–F coupling efficiency. We conducted a spatial correlation analysis to measure the results. This study demonstrated that the overall regional and interprovincial W–E–F coupling efficiency was low, with food subsystem as the main reason for low efficiency in the entire system and key reason for regional differences. When comparing the three subsystems, the efficiency value of the water resources subsystem showed little change over time. In 2015, the water resource efficiency in most regions reached an effective and effective marginal state. The efficiency of the energy subsystem and the food subsystem is on the rise. Overall, the food subsystem's efficiency is low, and in 2015, the food efficiency of several regions in northwest China was between 0.2–0.4 Spatial agglomeration was detected in W–E–F coupling efficiency in various regions of China. From a local spatial differentiation perspective, the proportion of the low–low (LL) space-related agglomeration pattern and high–high (HH) agglomeration was substantial. The LL agglomeration was primarily concentrated in the western and central underdeveloped areas, and a relatively stable space distribution of HH agglomeration occurred mainly in the eastern region.