The mountainous regions of southwest China represent one of the world’s most distinctive and sensitive areas. Against the backdrop of rapid urbanization and water conservancy construction, rural landscapes in these regions face challenges such as fragmentation, homogenization, and loss of local distinctiveness. Responding to the initiative of the European Landscape Convention (ELC), this study takes the Longchuan River Basin in Southwest China as a case study, and constructs a rural Landscape Character Assessment (LCA) framework adapted to the multi-level governance system. We established a multi-scale evaluation system covering large scale (county-level), medium scale (township-level), and detailed scale (reservoir area-level). The large scale integrated 6 categories of natural variables, while the medium scale involved 4 categories of natural variables and 4 categories of cultural variables. Using a Principal Component Analysis–Two-Step Clustering coupled method and eCognition software, landscape character types and areas were identified respectively. The results show that 11 landscape character types and 41 landscape character areas were identified at the large scale, and 6 landscape character types and 73 landscape character areas at the medium scale. At the detailed scale, 4 typical reservoir areas were selected for field surveys, which verified the in-depth impact of hydropower construction on landscape characteristics. The study provides a transferable technical pathway and policy recommendations for monitoring and managing rural landscapes in mountainous regions. Supports the long-term sustainability and resilience of rural landscapes in China.