<p>As a crucial aspect of urban development, urban interconnected river–lake system protects the city's ecological environment, enhance residents’ well-being, and stimulate economic growth. Scientific quantification and accurate evaluation of the project's ecological economic benefits are crucial for refining river and lake water system patterns and fostering the harmonious coexistence of economy, society, and ecology. However, the current traditional economic methods are unable to quantify the eco-environmental benefits objectively and directly, while the comprehensive evaluation method lacks pertinence in effect evaluation. In view of this, the emergy theory of eco-economic is employed to quantify the benefits and evaluate the effects of urban interconnected river–lake system. Then, based on the requirements of modern urban construction, the emergy indexes are proposed to evaluate the effects of urban interconnected river–lake system from six aspects: water security, water ecology, water engineering, water landscape, water culture and water management. Taking the Qingyi River interconnected river–lake system as an example, the engineering benefits and engineering effects from 2016 to 2020 were evaluated. The results showed that the project had particularly significant effects on water ecology, water engineering, water culture, water management, and water landscape, while the effect on water security was relatively weak. From 2016 to 2020, due to the eco-economic effects of the urban interconnected river–lake system, the unsustainable situation of the Qingyi River is gradually decreasing.</p>