Against the background of dramatic climate change, resource constraints and industrial upgrading, optimising the coupling and coordination of the water-energy-food (WEF) system in the northeast region is crucial to ensuring regional security and sustainable development. Existing research lacks long-term continuity and inter-provincial analysis. This article uses data from 2005 to 2023 to evaluate the development of the three northeastern provinces through 24 index frameworks covering safety, coordination and resilience. The methods include entropy weight method, coupling coordination model and constraint model. The result shows: (1) The overall development level fluctuates and has an upward trend, reaching a medium-coordinated level, and there are significant differences between provinces. (2) Coordination initially differentiated, and then gradually converged. From close to the improvement of the disorder to the level of moderate coordination, Liaoning Province declined under the impact of policies. (3) Systemic obstacles are structural and cross-regional, with energy self-sufficiency and water efficiency as key limiting factors. In order to achieve a high level of coordination between water, energy and food systems, it is necessary to formulate tailor-made subsystem governance policies, enhance the technological empowerment of water and energy conservation and efficiency improvement, and promote the development of resilient infrastructure. This integrated approach will systematically resolve resource competition conflicts, thus enhancing the overall resilience and sustainability of regional development.