Assessing the distribution of nature reserves is an important step for conserving biodiversity. We used geographic information system (GIS) to assess the conservation status of vegetation types, endangered plant and animal species, and biodiversity hotspots in China, based on the area, endangered species list and geographic position of 2,047 nature reserves in China. The results showed that, while the proportion of total area protected as nature reserves is higher in China than the world average, of the 47 natural vegetation types in China, 21 (45% of the total) were deficiently protected, with less than 10% of their area included in nature reserves, suggesting that these vegetation types have not been perfectly protected. According to the Dobson complementary algorithm, among 216 nature reserves, the top five priority nature reserves, i.e., Xishuangbanna, Mt. Wuyi, Mt. Changbai, Mt. Gaoligong and Mt. Qilian, contained 381 protected species (~ 50% of the total), and the top 21 priority nature reserves contained 590 protected species (~75% of the total). Nature reserves covered nearly all the hotspots selected by different approaches. However, as there are several areas lacking proper protection, e.g., Northern Xinjiang, Sichuan and South of the Yangtze River, the distribution of Chinese nature reserves needs further improvement.