With complex topography and geomorphology, mountainous cities possess abundant natural resources. They are constrained by ecological environment and topographic conditions, leading to a prominent contradiction between urbanization development and ecological protection. As a result, ecosystem services (ESs) are under greater regulatory pressure. The identification of ecosystem services bundles (ESBs) can be the foundation for developing zonal ecological protection planning policies. We took Chongqing as a case study, investigated the impact mechanisms of socio-ecological factors on the level of ES supply in each ESB. The findings reveal that: (1) The quantitative assessment of ESs for 2000, 2010, and 2020 showed that ESs were temporally stable and spatially heterogeneous. Areas with high supplies of food production (FP) and water yield (WY) were predominantly found in the northwestern cropland and urban built-up regions, whereas high supply areas for the other four ESs were primarily located in the northeastern Dabashan Mountains and the southern Wuling Mountains. (2) The quantification of trade-offs and synergies between ESs showed that FP had a trade-off effect with all five other ESs, while most other ES pairs exhibited synergistic effects. It was found that the interrelationships produced changes over time. (3) Then, three types of ESBs were identified. After examining the influence mechanisms of socio-ecological factors across the three ESBs, individual ESs were found to have essentially the same types of main impact factors in three ESBs, but varies in impact. (4) Finally, with reference to changes in ES levels and interrelationships and the driving mechanisms of socio-ecological factors in each zone, this study proposed zonal strategies for managing ecosystem services and optimizing territorial space based on the geographic characteristics and socio-economic development in different ESBs, with the goal of attaining sustainable urban development and improving human welfare.