Water resources, energy, and food are essential for the development of society, and they are strongly interdependent. The coupling and coordination relationships of the water–energy–food (WEF) system are important for regional resource security and high-quality development. The Yellow River Irrigation Area in Shandong Province, China, is a grain production base and has a substantial impact on national food security. To examine the water, energy, and food subsystem dynamics in this area, an evaluation system for the WEF system was established. A comprehensive weighting method based on game theory was employed to determine index weights. TOPSIS was used to assess the development level of the WEF system. A coupling coordination degree model was used to analyze the evolution of the coupling coordination degree of the WEF system from 2000 to 2020, and a GWR model was constructed to explore the spatial heterogeneity of its driving factors. The findings indicated that the development level of the WEF system in the study area was moderate, with a gradual upward trend. The coupling coordination degree fluctuated between 0.62 and 0.739. The GWR model revealed that temperature had an overall negative effect on the coupling coordination degree, with the greatest impact on the central irrigation area; the slope and NDVI had a negative effect, with increasing intensity from the southwest to the northeast; and rainfall had an overall positive effect, with the greatest impact on the irrigation area near the estuary in the northeast. Overall, the building area ratio had a negative effect on the coupling coordination degree, with exceptions in some areas. These research outcomes provide theoretical support for sustainable agricultural development in the Yellow River irrigation areas of Shandong Province and methodological reference data for studying collaborative resource utilization in irrigation regions.