Based on the theory of comparative advantage, this paper analyzes the major challenges facing the development of green economy in China's mountain regions. The results show that in the development of green economy, the mountain regions have factor endowment and development conditions with comparative advantage, but they are also facing more challenges. In the future, the mountain regions need to make favorable development measures based on their own comparative advantages from the following four aspects: at the top design level, it is necessary to ensure green development through institutional innovation; at the regional level, it is necessary to lead green development through the differentiation strategy; at the industrial level, it is necessary to support green development through transformation and innovation; at the social level, it is necessary to focus on protecting vulnerable groups and give full play to the role of women to promote sharing of green development results.