Until 2015, China had established 2740 nature reserves with a total area of 1.47 million km2, covering 14.8% of China’s terrestrial land surface. Based on remote sensing inversion, ecological model simulation and spatial analysis methods, we analyzed the spatial and temporal variations of fractional vegetation coverage (FVC), net primary production (NPP), and human disturbance (HD) in habitats of typical national nature reserves (NNRs) during the first 15 years of the 21st century from 2000 to 2015. And then the three indicators were compared between different NNR types and varied climate zones. The results showed that (1) the average 5-year FVC of NNRs increased from 36.3% to 37.1%, and it improved in all types of NNRs to some extent. The annual average FVC increased by 0.11%, 0.84%, 0.21%, 0.09%, 0.11% and 0.08% in NNRs of forest ecosystem, plain meadow, inland wetland, desert ecosystem, wild animal and wild plant, respectively. (2) The NPP annually increased by 2.06 g·m-2, 1.23 g·m-2, 0.28 g·m-2 and 0.4 g·m-2 in NNRs of plain meadow, inland wetland, desert ecosystem and wild animal, respectively. However, it decreased by 3.45 g·m-2 and 2.35 g·m-2 in NNRs of forest ecosystem and wild plant respectively. (3) In the past 15 years, besides the slight decreases in the NNRs located at the Qinghai-Tibet Plateau and the south subtropical zone, HD enhanced in most of NNRs, especially HD in the warm temperate humid zone increased from 4.7% to 5.35%.