Water, energy and food (WEF) are important strategic resources for economic development in arid agriculture-based regions. Analyzing development indicators in the management of limited resources to achieve sustainability on a time scale is one of the basic goals of this research. Therefore, a system dynamics model was developed to analyze the WEF system resource flow relationship to achieve sustainable resource development. First, the subsystems of WEF resources were created and their dynamic relationship was formed in the form of a logical loop in a 10-year time frame. The evolution of 7 years (from 2015 to 2022) was taken into consideration to predict the 3-year period (from 2023 to 2025). The results showed that the reduction of water resources exploitation rate in China in interaction with agricultural productivity has automatically improved energy consumption and the nexus index. In China, a dynamic balance between WEF with a focus on water is recommended for planning.