The coordinated development of urban energy-economy-environment (3E) systems is an inherent requirement for high-quality and sustainable development of cities. Circulation degree and sustainable development degree (SDD) are combined to the previous 3E system evaluation system to construct the integrated sustainable development evaluation model. This model realizes the accurate evaluation of different dimensions of 3E system. Jinan, the capital city of Shandong Province in eastern China, is selected for empirical analysis. Findings show that development degree, circulation degree, and SDD of the 3E system in Jinan are increasing basically, and temporal trend of development degree and SDD of 3E system is synchronized. This shows that 3E system in Jinan has been improved gradually during this period, and the development of 3E system is a key factor affecting its sustainability. In 2015-2017, circulation degree and SDD were superimposed and developed in parallel, indicating that Jinan has entered the primary stage of high-quality development. The obstacle degree model is introduced to explore the main factors that impede the sustainable development of 3E system in Jinan. This study revealed that the energy consumption structure, the proportion of new energy utilization, the development of tertiary industry, and water resources protection are the key issues that should be addressed in the sustainable development of 3E system in Jinan. The top-level design concerning these issues should be highlighted in the forthcoming 14th five-year plan period.