The most direct and effective way of protecting biodiversity and their habitats is to establish nature reserves. It has become critically important to establish a comprehensive scientific evaluation index system to assess protection efficacy and promote effective management of China's national nature reserves. Currently, a large number of nature reserves or protected areas have been established worldwide. However, human disturbance and invasion by alien species and other detrimental factors have undermined the ecological benefits of these original habitats. For example, migratory birds still face destruction of their breeding sites, loss of their wintering and stopover sites, and poaching of their non-breeding sites. As of March 2014, 105 national nature reserves specifically for wildlife had been established in China out of a total of 407 national nature reserves. Of these wildlife nature reserves, 22 are designated for migratory birds as the first target of protection through the provision of various kinds of food, habitat, and breeding sites for these birds. Although the Chinese Government has invested a lot of manpower, material, and financial resources in national reserves, their protection efficacy remains unclear. It is, therefore, critical at this juncture to evaluate the protection efficacy of China's national nature reserves for migratory birds to assess their achievements and identify problems, improve effective management effectiveness and biodiversity conservation, and take macroscopic decisions. Different scales of time and space lead to different evaluation results of protection efficacy. We used three methods: integrated analysis, expert consultation, and a case study to develop the first indicator system for evaluating protection efficacy of national nature reserves for migratory birds over the past ten years. The indicator system included one target layer, two system layers (evaluation of conservation effectiveness with a 60% score, and evaluation of management effectiveness with a 40% score), nine factor layers, thirty-six index layers, and seven assigned indexes of anthropogenic influence (-12 points to +8 points). Factor layers of the evaluation of conservation effectiveness included representativeness, suitability, rarity, diversity, and integrity. Factor layers of the evaluation of management effectiveness included management objects, actions, security, and effectiveness. Among the index layers, the number of target species, habitats, water, shelter environments, food resources, routine patrols, environmental quality, and human activities were the focus areas of the indicator system for evaluating protection efficacy. To verify and perfect the evaluation index system, we carried out a case study of the Qinghai Lake National Nature Reserve (QLNNR) and the Hunan East Dongting Lake National Nature Reserve (EDLNNR). The results showed that the evaluation index system demonstrated good scientificity and operability. QLNNR has performed very well in terms of target species monitoring, publicity and education, field patrol, and co-management. However, ecotourism has had some impacts on the activities of migratory birds, so management in this area requires strengthening. EDLNNR has been successful in the areas of publicity and education and field patrol. However, a lack of clarity about land ownership has resulted in a series of adverse consequences. There is, therefore, a need to strive for clarity in terms of land ownership, establishing effective management, and developing ecotourism to improve residents' incomes, and reduce anthropogenic influences to restore the habitats of migratory birds.