Water resources, energy, and food are fundamental resources for high-quality regional development. In the process of rapid regional economic growth, integrating the utilization of these fundamental resources has become a critical challenge for achieving high-quality development in the Ili River Valley. To explore the coordinated development status of water, energy, and food (W-E-F) in the Ili River Valley, we constructed a comprehensive evaluation indicator system for the regional W-E-F system, and we calculated and analyzed the comprehensive development level, coupling coordination degree, and spatial equilibrium of the W-E-F system from 2008 to 2020. The results indicate that the comprehensive evaluation indicators of the W-E-F system in the Ili River Valley exhibited an overall upward trend, indicating that the system is moving in a positive direction. Among them, the water subsystem’s comprehensive evaluation indicator showed an upward trend but fluctuated significantly during the study period, with the excessive proportion of agricultural water consumption being a key factor affecting its development. Furthermore, the comprehensive evaluation indicator of the energy subsystem showed a slight downward trend, indicating constraints on the development of energy subsystems. Agricultural surface pollution and industrial waste pollution are the primary factors limiting its development. Meanwhile, due to the significant attention from governments at all levels, the food subsystem has been developed rapidly, with its comprehensive evaluation indicator showing a significant upward trend, which shows that the region is actively promoting food production capacity enhancement initiatives. Additionally, the coupling degree of the W-E-F system remained in a state of coordinated coupling, with an average value between 0.7 and 1.0, indicating a high overall development level, and that the development of each resource affects and constrains that of the other two. The coupling coordination degree transitioned through phases of near coordination, primary coordination, good coordination, and moderate coordination, and all counties and cities showed a tendency to evolve towards high coupling, indicating significant potential for the further development of the regional W-E-F system coupling and coordination. Among the subsystems, the food subsystem exhibited the highest spatial equilibrium (0.78) and the smallest spatial disparities, while the energy subsystem demonstrated the lowest spatial equilibrium (0.40) and the largest spatial disparities. There were still significant issues with the utilization and equilibrium of the regional resource allocation, necessitating integrated planning for the coordinated development of the W-E-F system to achieve sustainable resource management and high-quality ecological and economic development.