By analyzing basic characteristics of mountainous river systems, this paper established an index system of mountainous river health assessment from both an ecological service perspective and the perspective of meeting human needs, and has built a mountainous river health evaluation model based on Projection Pursuit theory. Taking a typical mountainous river in southwestern China as an example, this paper investigated its health status prior to and after hydropower development. The result showed that the comprehensive health situation after hydropower development is significantly better than that in the current situation. In addition, this paper proposed countermeasures for river health maintenance based on an analysis of structural features of the evaluation result.