Water, energy and food are three important resources for human to face serious security risks. A systematic perspective, namely Water, Energy and Food Nexus (WEFN), was proposed to achieve the sustainable human development. In this study, a method of hierarchical weight assignment based on synergetic theory and Shannon information theory was applied in the Bayan Nur city, China. Through calculating order degree of order parameter components of resources, society, economic and environmental dimensions, the order degree of order parameters and sub-systems and the order entropy were obtained. It is found that water resources supply, energy supply, energy consumption and food price would dominate the corresponding trends in water, energy and food sub-systems respectively. The water and food sub-system may play a more dominant role in the harmonious assessment of WEFN system in the study area. Although the variance of the order degree of sub-systems and the order entropy were small, the WEFN system was still moving toward an unstable state, which could aggravate the inharmonious degree of WEFN system in the study area.