The Three Gorges Reservoir Area (TGRA) serves as a crucial ecological barrier in the upper reaches of the Yangtze River and represents a typical ecologically sensitive region. Studying the changing characteristics of urban ecological elements in the reservoir area is of significant importance for maintaining regional ecological security and implementing ecological restoration. Focusing on Zhongxian County, Chongqing Municipality, during the period 2000–2020, this study identifies ecological networks and habitat quality levels for three distinct periods using Morphological Spatial Pattern Analysis (MSPA), Circuit Theory, and the InVEST model. It explores the spatiotemporal evolution characteristics of the ecological spatial pattern in reservoir-region urban areas and proposes targeted optimization strategies for ecological conservation redlines. The results reveal that: (1) The overall ecological environment in Zhongxian County showed improvement trends over time. The number of ecological sources increased from 12 to 48, with their combined area expanding from 131.13 km2 to 351.03 km2. These sources exhibited a clustered distribution in the central region. Ecological corridors increased from 23 to 112. While corridor length initially rose from 191.55 km to 314.94 km, it subsequently fluctuated downward to 292.99 km. Spatially, corridors displayed a denser distribution in the north and east compared to the south and west. (2) The habitat quality indices for the three periods were 0.3311, 0.3841, and 0.3816, respectively, indicating an initial increase followed by a slight decline. Overall, habitat quality demonstrated improvement. Central areas rich in forest resources exhibited higher habitat quality, whereas areas along both banks of the Yangtze River and the central urban core showed poorer habitat quality. (3) A synergistic relationship exists between the spatial distribution and changes of ecological network elements and habitat quality levels, with land use structure changes exerting the most significant influence. (4) A zoned management strategy was implemented for ecological sources, alongside optimization of Ecological Protection Redline (EPR) boundaries. Following boundary adjustments, the designated EPR area covers 124.72 km2, while 125.57 km2 and 189.81 km2 were demarcated as compensation zones and reserve zones, respectively. The findings provide a scientific reference for advancing high-quality green development in urban-rural integration zones within the Three Gorges Reservoir Area under the Yangtze River Conservation Initiative.