Nature reserves provide the cornerstone of most national strategies to conserve biodiversity, and establishing nature reserves is perhaps the most important of all conservation tools focused on the preservation of wildlife habitat. Human encroachments and threats are generally perceived to be very common in many nature reserves. Therefore, it is necessary to assess variation in the ecosystem patterns of national nature reserves. To reveal ecosystem composition structure and its variation in national nature reserves of China, based on the ecosystem transition types and extents, and considering the importance of different functional zones in the nature reserve, we developed an ecosystem pattern variation index to examine the dynamic change of the ecosystem pattern, using ecosystem distribution data collected in 2000 and 2010 for 319 national nature reserves. The results showed that the grassland ecosystem accounted for the largest area, comprising 57.88% and 57.74% of the total area of the ecosystem in national nature reserves in 2000 and 2010, respectively, followed by the desert ecosystem, accounting for about 17% both in 2000 and 2010, and then wetland, forest, shrub, field, glacier and permanent snow, marine and town ecosystems successively. From 2000 to 2010, the area of forest and wetland ecosystems showed obvious increases, and the town expanded to some extent, but the glacier and permanent snow ecosystem decreased appreciably in the national nature reserves. Overall, the ecosystem pattern of nature reserves essentially remained stable. There were 219 nature reserves that showed stability, accounting for 68.65% of the total. The number of nature reserves tending to improve was slightly higher than the number of those tending to degenerate. These results reflect the fact that ecosystem conservation in national nature reserves has been effective to a certain extent. The improved nature reserves were mostly distributed in Qin Mountain, Daba Mountain, Dalou Mountain and South Mountain, while the degenerated nature reserves were mostly distributed in the eastern provinces, Inner Mongolian Plateau and the northeast plain. The degenerated nature reserves were mainly desert ecosystems, inner wetland and aquatic ecosystems, reserves for the protection of wild animals, and natural monuments. Finally, we put forward three suggestions to improve the management level for national nature reserves.