The number, area, and development speed of China's natural reserves have reached the top in the world and are higher than the global average. The total area of more than 2740 natural reserves accounted for approximately 14.8% of the land area in China. In this study, 446 national natural reserves were selected as study areas, which accounted for 65.9% of the total area of China's nature reserves. Based on the methods of remote sensing information extraction, model and equation estimation, and spatial and temporal analysis, the spatial and temporal patterns of ecosystem quality and key services from 2000 to 2015 in different types of natural reserves and varied regions in natural reserves were analyzed. Then, the anthropogenic activities and their effects on ecosystem quality and services were analyzed through quantified land cover changes. The results showed that:(1) The obvious land cover changes in the National Nature Reserves indicated that there were different degrees of human activities, which were more aggressive outside the nature reserves than inside them. It also indicated that the nature reserves have obvious protective effects on the ecosystems; (2) The negative effects of human activities, such as farmland reclamation, residential construction, industrial and mining construction, and energy resources development on the ecosystem of the reserves were as follows:reclamation of grasslands and wetlands increased the cultivated land area by 894.8 km², development of reservoirs and ponds decreased the cultivated land area by 290.4 km², expansion of urban residential, and industrial and mining construction land mainly occupied the grasslands by 51.3 km² and 169.1 km², respectively;(3) wetland area increased by 281 km², forests and grasslands had a net decrease of 145.8 km² and 1531.5 km², respectively, which reflected the positive effects of wetland protection and returning farmland to lakes, but the effects of returning farmland to forest and grasslands were limited to some nature reserves;(4) climate change was the main reason for the weak increase of vegetation coverage, the decrease of net primary productivity, the slight increase of ecosystem water conservation, and the significant increase of ecosystem soil conservation; however, human activities only effected the ecosystem locally. To promote the development and protection of China's nature reserve system, it is necessary to unify the standards and specifications of the nature reserve system, improve the legal system of nature reserves, and promote basic scientific research.