On the basis of Chinese Traditional Villages Assessment Indicator System and field research of southwest mountainous villages, this paper, putting the ambiguity of protection and evaluation of mountainous traditional villages, provides adjustments and supplements for the existing evaluation system. It has established criteria collection of the mountainous villages’ protection and evaluation, and has ensured the weight of evaluation indicator with the mathematical logistic approach. It also effectively combines the qualitative and quantitative analysis, ensuring the reliability, accuracy and objectivity of evaluation indicators. Hence it eventually establishes evaluation indicator system of the evaluation of the traditional villages in mountainous region.