Abstract: Clarifying the impact of rural tourism development on the trade-offs and synergies of ecosystem services (ES) is crucial for balancing ecological protection and regional sustainable development. Taking the Qinba Mountain Area in southern Shaanxi Province as a case study, this paper uses data from 2012, 2017, and 2022. The InVEST model, Pearson correlation coefficient, and root mean square error (RMSE) were integrated to evaluate the spatiotemporal variations of ES and their trade-offs/synergies. The spatiotemporal distribution of rural tourism was characterized using kernel density analysis of Points of Interest (POI), and the Geographical Convergent Cross Mapping (GCCM) model was employed to reveal their interactive effects and evolutionary mechanisms. The results show that from 2012 to 2022, the interaction between rural tourism and ES trade-offs/synergies continuously strengthened, evolving from an initial unidirectional influence into a bidirectional feedback relationship, with a steady increase in coupling intensity. In 2012, although the development intensity of rural tourism was low, it already exerted a significant effect on the synergy between water yield and habitat quality, indicating an emerging ecological effect. By 2017, the unidirectional influence of rural tourism extended to the relationships between water yield–soil conservation and soil conservation–habitat quality, while bidirectional feedback appeared in the relationships between water yield–habitat quality and carbon sequestration–habitat quality, reflecting the deepening of the feedback mechanism and the emergence of an ecological resource orientation. In 2022, the feedback mechanism further intensified: the interactions between rural tourism and the relationships of soil conservation–habitat quality and carbon sequestration–habitat quality transformed into an ecological resource-driven model, and the scope of rural tourism’s influence on ES trade-offs/synergies expanded to four pairs. This study provides a scientific basis for the coordinated management of rural tourism and the ecological environment in key ecological function zones.