Traditional villages possess a sustainable spatial structure through their harmonious symbiosis with natural landscapes. The northwest region of Yunnan Province is characterized by a rugged terrain and diverse landforms. Influenced by the integration of multiple cultures, traditional villages in this area display a variety of settlement spatial forms and ecological wisdom. This study selects two representative traditional villages located in the northwest of Yunnan: Niyu Village and Stone Town Village. Combining literature review and field research, it analyzes the ecological wisdom embedded within these villages from the perspective of the “five living ecological space”, habitat, production, life, and vitality. It reveals the unique ecological wisdom demonstrated by the two villages in terms of landscape layout, spatial arrangement, production clusters, residential construction, and folk customs. A comparative analysis is conducted to highlight their differences. On this foundation, corresponding protection and development strategies are proposed to facilitate the protection and sustainable development of various types of traditional villages in northwest Yunnan, thereby offering valuable experience and inspiration for modern rural construction.