According to the problem of seriously degraded natural forest in Southwest China prior to the implementation of Natural Forest Protection Project, under the guidance of principle of practicality and systematicness, we establish the comprehensive-benefit evaluation index system of restoring the degraded natural forest in Southwest China, including 3 second-level indices, 12 third-level indices and 24 fourth-level indices. In addition, we use the method of Analytic Hierarchy Process to conduct comprehensive-benefit evaluation on implementation of Natural Forest Protection Project in Southwest China. The results show that since ten years of implementation of Natural Forest Protection Project in Southwest China, it has gained considerable comprehensive benefit. The comprehensive evaluation index of Natural Forest Protection Project in Southwest China is 83.08; the ecological benefit index of Natural Forest Protection Project in Southwest China is 56.75; the economic benefit index of Natural Forest Protection Project in Southwest China is 19.05; the social benefit index of Natural Forest Protection Project in Southwest China is 7.28. The effect of construction of Natural Forest Protection Project in Southwest China is good. The evaluation index system and research results in this paper will provide the empirical guidance for comprehensive-benefit evaluation of Natural Forest Protection Project in China, and especially in Southwest China.