Natural forest resources are important strategic and ecological resources in China, which play an irreplaceable role in maintaining the eco-security of the national territory, mitigating climate change and protecting biodiversity. Since its full launch in 2000, the Natural Forest Protection Program (NFPP) has had a huge impact on the forest resource conservation and restoration,ecological environment improvement, regional economic and social sustainable development in the upper reaches of the Yangtze River, the upper and middle reaches of the Yellow River, as well as key state-owned forest regions in Northeast China, the Inner Mongolia, Xinjiang, and Hainan. The second phase of NFPP was successfully completed in 2020, and thus, it is the time to carry out a comprehensive assessment of the multiple-dimension effects and impacts of NFPP, which can provide decision-making basis for updating relevant policies and scientific support for comprehensively promoting the protection and restoration of natural forests. To evaluate the implementation effectiveness of NFPP, this paper elaborated a comprehensive system of methodology that include the five dimensions in terms of forest resource, ecological benefit, social and economic benefit, ecological restoration measures and policy design. Several approaches in terms of spatial information technology, sample plot survey, ecological station observation, comparative analysis and other methods were employed and developed for the quantitative assessment of NFPP. This evaluation system will be of great significance to the overall implementation of the National Eco-civilization Strategy and 《Natural Forest Protection and Restoration System Plan》, and provide good guidance and reference for the national major ecological project evaluation.