The Three Gorges Reservoir Area is a social-ecological system integrating rural and mountainous areas. Studying the interaction within the system and the coupling transformation between the systems is conducive to promoting the high-quality sustainable development of the reservoir area. By constructing the research framework of social-ecological system coupling transformation, using the methods of topographic potential index and coupling coordination degree model, so as to reveal whether the social-ecological system transformation is or not, the diversity of transformation paths and its driving mechanism in the Three Gorges Reservoir Area. The results show that:(1) from 2000 to 2020, the quantity, structure and function of the social-ecological system in the Three Gorges Reservoir Area have changed significantly, indicating the transformation of the social-ecological system in the reservoir area. (2) The social-ecological system of the lowland position in the reservoir area changed from social-ecological type to ecological economy type, the median position changed from ecological social type to ecological dominant and ecological economy supplemented, and the highland changed from ecological regulation type to ecological dominant type. (3) The change of farmers' and government's demand is the fundamental factor driving the transformation of social-ecological system from traditionally cultivated land planting system to new economic fruit forest planting system. (4) The research method of this paper proves that it is universal to mountainous areas, and the research framework is more suitable to describe the transformation path of social-ecological system in mountainous areas, which can also be applied in other places.