Historic towns and villages in mountain areas are important types of historical and cultural heritages with both dominant cultural and hidden ecological attributes. Its ecological and cultural protection should take into account the concerns, which embody the recognition and respect to ecological relationship in such heritage, and emphasizes the basic position and role of ecological protection in the heritage conservation. Based on the association with the historical environment, historic towns and villages in mountain areas have its special ecological problems and research priorities. This paper, taking Bayu area as an example, summarizes the ecological characteristics of historic town and village in mountainous areas, revealing the main issues in the current protection. On the basis of determining the objectives and principles of ecological protection, this paper studies the ecological protection from two levels of ecological landscape and ecological security pattern, proposes the overall strategy and technology framework on protection, sums up the technical points of solving ecological issues on historic town and village in mountainous areas, and explores the protection mode under the mountain ecological perspective as well as enriches the current protection theory of historic town and village in mountainous areas.