Water, energy, and food (WEF) are critical resources to sustain urban development, which requires a sustainable structure of the urban WEF nexus to address trade-offs and achieve synergies. Although interactions in the WEF nexus are widely explored, its sustainable structure has largely been ignored. This study constructs a framework of WEF nexus sustainability factors. Based on a literature review and expert opinions, 21 factors influencing urban WEF nexus sustainability were extracted and their interrelationships determined. We used social network analysis (SNA) and interpretive structural modeling (ISM) to analyze the structure of the urban WEF network. The results indicate that technological investment and industrial added-value energy consumption are the most critical and fundamental factors for promoting the sustainable development of the urban WEF nexus. Additionally, the balance of water supply and demand and the comprehensive management of waste pollutants are also driving and supporting factors for the sustainability of the urban WEF nexus. The results of this study complement the interaction mechanism research of the urban WEF nexus and provide practical references for sustainable decision-making in urban WEF nexus practices.