The Three Gorges Reservoir Area (TGRA) is an important ecological barrier and cultural intermingling zone in the upper reaches of the Yangtze River, and its traditional villages carry unique information about natural changes and civilisational development, but face the challenges of conservation and development under the impact of modernisation and ecological pressure. This study takes 112 traditional villages in the TGRA that have been included in the protection list as the research objects, aiming to construct a cultural landscape identification framework for the traditional villages in the TGRA. Through field surveys, landscape feature assessments, GIS spatial analysis, and multi-source data analysis, we systematically analyse their cultural landscape type systems and spatial differentiation characteristics, and then reveal their cultural landscape types and spatial differentiation patterns. (1) The results of the study show that the spatial distribution of traditional villages exhibits significant altitude gradient differentiation—the low-altitude area is dominated by traffic and trade villages, the middle-altitude area is dominated by patriarchal manor villages and mountain farming villages, and the high-altitude area is dominated by ethno-cultural and ecologically dependent villages. (2) Slope and direction analyses further reveal that the gently sloping areas are conducive to the development of commercial and agricultural settlements, while the steeply sloping areas strengthen the function of ethnic and cultural defence. The results indicate that topographic conditions drive the synergistic evolution of the human–land system in traditional villages through the mechanisms of agricultural optimisation, trade networks, cultural defence, and ecological adaptation. The study provides a paradigm of “nature–humanities” interaction analysis for the conservation and development of traditional villages in mountainous areas, which is of practical value in coordinating the construction of ecological barriers and the revitalisation of villages in the reservoir area.