Vegetation cover change is a dual indicator of climate change and ecological environment change, How to quantify vegetation cover change at the national scale and evaluate the effectiveness of ecological restoration has become a common scientific issue in the current field of terrestrial surface ecosystem research. This article used vegetation coverage (FVC) data from 2000 to 2020, the methods of incremental change analysis, Theil Sen Median trend analysis, and stability analysis to study the background and spatiotemporal changes of natural vegetation coverage in six national key ecosystem protection and restoration project areas in China. The correlation between vegetation coverage changes in different regions and temperature and precipitation was also analyzed. The results showed that:(1) In 2020, the average vegetation coverage of the six major regions was 27.66%. From 2000 to 2020, the growth rates of the key ecological area of the Yellow River, the northern sand prevention zone, and the ecological barrier area of the Qinghai Tibet Plateau were 54.4%, 34.6%, and 21.8%, respectively, which was 1.04 to 2.59 times of the national average vegetation coverage growth rate; The growth rates in the key ecological area of the Yangtze River, the northeast forest belt, and the southern hilly mountain zone were 18.0%, 13.7%, and 12.9%, respectively, which were lower than the national growth rate. The improvement was more obvious in the northwest of China than in the south. (2) From 2000 to 2020, the overall vegetation coverage changes in the six major regions showed an increasing trend. The proportion of increased areas in the key ecological areas of the Yellow River, northeast forest belt, southern hilly mountain zone, and Yangtze River exceeded 60%. The proportion of increased vegetation in the northern sand prevention zone and the ecological barrier area of the Qinghai Tibet Plateau was relatively low, with 24.9% and 17.6%, respectively, vegetation change was significantly affected by human activities. (3) The changes in natural vegetation coverage in the six major regions were relatively stable, with the main variation areas located in the ecological barrier area of the Qinghai Tibet Plateau, the northern sand prevention zone, and the key ecological area of the Yellow River, which were more influenced by natural factors such as climate and geological disasters. (4) There were differences in the correlation between vegetation coverage changes and precipitation and temperature in different restoration areas. The correlation between FVC and annual precipitation was not significant in the ecological barrier area of the Qinghai Tibet Plateau, the key ecological area of the Yangtze River, and the southern hilly mountain zone, but it was significantly correlated with annual average temperature. The vegetation coverage change in the northern sand prevention zone was significantly correlated with annual precipitation, but not with annual average temperature; There was no significant correlation between the vegetation coverage changes in the key ecological area of the Yellow River and the northeast forest belt and the annual average temperature and precipitation.