Abstract: The Three Gorges Reservoir Area (Chongqing section) is one of the segments in the upper reaches of the Yangtze River ecological barriers. Rapid urbanization has posed a significant challenge to balancing human activities and ecosystem services in recent years. Regional ecological security can depend mainly on the water and flood control in the National Key Ecological Function Zone and the priority area for biodiversity conservation in the middle and lower reaches of the Yangtze River. Land use has also encroached on the ecological space under the Three Gorges Project and urban expansion. Fortunately, ecological restoration has alleviated the pressures, such as grain-for-green and shelterbelt construction. It is often required for the increasingly diverse demands on the ecosystem under the spatial expansion of urbanization. However, conventional ecosystem service is predominantly limited to assessing the supply-side economy valuation and supply–demand relationships. In this study, a three-tier conflict–adaptation framework was developed to assess the ecosystem services. The Millennium Ecosystem Assessment framework was also integrated with Schwartz's theory of human values. The Chongqing section of the reservoir was applied from 2006 to 2015 and 2024. The framework was used to examine: 1) the interactions among seven supply services (Water yield, Food production, Carbon storage, PM₂.₅ removal, Landscape aesthetics supply, Habitat quality supply, and Soil conservation supply); 2) value–driven dynamics among seven demand services (Water demand, Food demand, Carbon emissions, PM_2.5 exposure risk, Landscape aesthetics demand, Habitat quality demand, and Soil conservation demand); and 3) coupling between the function and capacity subsystem. Results reveal that there was a “scissors-shaped” spatial divergence: the high-conflict zones were concentrated in the metropolitan Chongqing and radiated southeastward along the main Yangtze channel, while the high-adaptation areas expanded southwestward from the northern mid-reservoir toward inland regions. Supply-side analysis indicated that the structural reconfiguration of the service relationship was weakened or reversed into trade-offs. On the demand side, the activities driven by the “hedonism–self-direction–stimulation” values (e.g., Carbon emissions and Landscape aesthetics demand) increasingly intersect with those rooted in the “security–tradition–universalism” (e.g., Water demand, Food demand, and Habitat quality demand). There was the society transition from the basic subsistence into material and experiential well-being, and from the single-dimensional evaluation to multi-system dynamic analysis. This framework was used to bridge the gap between human values and ecosystem service demands. Furthermore, the targeted strategies—such as the graded restoration in the conflict zones and radiation effects from the adaptation zones–were proposed to align with the specific value orientations for the Habitat quality demand and PM_2.5 removal. This approach can transfer for the river basins like the development–conservation tensions. Spatially explicit planning can also support the “mountains–rivers–forests–farmlands–lakes–grasslands–deserts” life community.