[Objective] Elucidating the coordination between ecosystem quality and service functions, along with its underlying mechanisms, represents a core scientific issue for supporting regional sustainable development. This study focuses on five key districts/counties in the Chongqing section of the Three Gorges Reservoir Area—a typical ecologically fragile zone and critical ecological functional region. It aims to bridge current knowledge gaps regarding the “quality–function” synergy and its driving mechanisms, thereby providing a scientific basis for ecological management in the reservoir area. [Methods] The InVEST model was employed to evaluate the water conservation function, and the RSEI model was used to quantify ecosystem quality. A coupling coordination degree model was applied to assess their synergistic relationship, while the Geodetector Detector method was adopted to quantitatively analyze the driving mechanisms of natural and socio-economic factors on the coordination state. [Results] ① Over time, ecosystem quality in the study area continued to improve, whereas water conservation volume first decreased and then increased, showing noticeable fluctuations. ② Spatially, the coordination level improved significantly, displaying a distinct geographical pattern of “higher in the periphery, lower in the center.”③ Driving analysis revealed that elevation and temperature were the dominant factors, and interactions among natural factors significantly enhanced the spatial heterogeneity of coordination degree. [Conclusion] The synergy between ecosystem quality and water conservation function has strengthened notably in the Chongqing section of the Three Gorges Reservoir Area. This coordination is driven nonlinearly by the coupling of natural factors and human activities. Accordingly, the study proposes implementing differentiated zoning strategies in future ecological conservation: strictly controlling development intensity in areas with high human disturbance, and strengthening vegetation restoration and water conservation capacity in ecologically sensitive mid-to-high elevation zones, so as to foster overall ecosystem coordination and regional sustainable development.