[Objective] Investigating the interactive coupling characteristics of the PEE system can provide theoretical support and quantitative basis for the ecological advancement of urban areas in the Three Gorges Reservoir Area. [Methods] Based on a comprehensive evaluation of the PEE system in the Three Gorges Reservoir Area from 2000 to 2020, this study utilized the coupling coordination degree model, gravity model, and obstacle degree model to empirically investigate the spatiotemporal evolution characteristics, spatial connectivity features, and main obstacle factors of the system’s coupling coordination degree. [Results] (1) The comprehensive development level of the PEE system in the reservoir area had shown a gradual increase from 2000 to 2020. (2) During the study period, the coupling and coordination degree of the system was basically unchanged, with a not very high level of coordination. The type of coordination showed the spatial characteristics of "Southwest-Northeast" and "Central-North", with an overall benign upward development trend. (3) The spatial correlation of the coupling and coordination degree of the system in neighboring regions had a significant positive autocorrelation, the total spatial linkage was rising in general, the spatial linkage strength was weak, and it was gradually weakening with the increase of the geographic distance. (4) The influence of each factor on the system’s development had a convergence, with the economic and demographic system being the main constraining subsystems, and the obstacle degree of the environmental system was increasing year by year. [Conclusion] The overall level of coupled and coordinated development of the PEE system in the reservoir area was improving, and regional differences were narrowing. In the future, the focus should be on the optimization of a single system to the coordination of multiple systems, and adjustments should be made from both the perspectives of the system itself and regional synergy, in order to strengthen policy and institutional regulation and scientifically explore the development path.