The coordinated development of the water-energy-food system is an important support for the sustainable development of economy and society. China’s ecological civilization is in a critical period of pressure superposition and load bearing. The contradiction between high resource pressure, limited environmental capacity and high total pollutant discharge is prominent, and the task of building a beautiful China is still arduous. Green development, as an important part of the new development concept, is the inevitable requirement of ecological civilization and the inevitable course to build a beautiful China. Exploring China’s resources and environment problems from the concept of green development actually provides a new idea for the practice of water-energy-food management. This paper starts from the internal mechanism of the impact of green development on water-energy-food system, and the complexity and dynamic characteristics of the system are considered in the construction of system dynamics model. The model better explains the evolution process of water-energy-food system under the influence of green development, and simulates the policy effectiveness and implementation strength under different green development guidance and constraint scenarios. The research finds that the adjustment and implementation of green development guidance and restraint policies can promote the water-energy-food system to reduce resource consumption and pollution emissions. Different policies implemented by the government have different effects. On this basis, combined with regional resource endowment and carbon peaking and carbon neutrality goals, we propose that the relevant departments should further optimize the binding policy environment for green development, increase the implementation intensity of green development policies, promote the efficient use of resources and reduce pollution stocks, and give full play to the policy efficiency of green development in resource management.