<p>The coordinated development of water resources, social economy, and ecological environment (WSE) in the irrigation district is fundamental to sustainable management and food security. In this study, a model is established to address the lack of effective methods for quantitative assessment and diagnosis of WSE coordinated development due to the complex and uncertain WSE structure. Therefore, an assessment model of WSE development is proposed by utilizing the structural analysis of WSE and connection number theory. This study adopts a mechanical model to assess the status of WSE coordination and diagnose the uncoordinated reasons, and a coordinated development assessment model is constructed using a risk matrix. Applying this method in five counties of the Dagong irrigation district of the Yellow River indicates average values of 0.403 (low development), 0.377 (medium slowness), 0.497 (low development), 0.572 (medium development), and 0.589 (medium development) for the WSE development degree in Neihuang, Xunxian, Huaxian, Changyuan, and Fengqiu, respectively, during 2010–2017, with average values of 0.677 (medium incoordination), 0.781 (low coordination), 0.611 (high incoordination), 0.797 (low coordination), and 0.842 (medium coordination) for the WSE coordination degree. Coordinated development status in the area deteriorates gradually from south to north, and although the overall situation has been improved, the differences among the five counties remain significant, with Neihuang and Huaxian being the most severe incoordination. Enhancing the advance of economy and environment, matching and promoting the support capacity of water resources condition, and maintaining a balance of these three sub-systems are the crucial points of coordinated development of the WSE structure in the Dagong irrigation district. This study provides targeted policy reference for water resources planning and effectively promotes the application of structural water resources science.</p>