China's investments, financial incentives and deductions on ecological conservation are based on the county level. Therefore, the monitoring and assessment on the effects of ecological conservation at the county level is significant to provide a scientific basis to the ecological and environmental quality assessment of counties. This paper quantitatively estimated the dynamics of high-quality ecosystems and the vegetation coverage in the past 15 years, and examined its relationships with the number of ecological conservation programs at the county level. Then it assessed and discussed the effects of ecological conservation measures in county's ecological changes and its regional suitability. The results showed that the proportion of high quality ecosystems higher than 50% was primarily observed in counties of Northeast China, subtropical southern China and southeastern Qinghai-Tibet Plateau, and the proportion lower than 20% was mostly found in counties of Northwest China, karst region of Southwest China and the North China Plain. In recent decades, ecological conservation focused on ecological fragile regions, so there are more than five ecological conservation programs in most counties of the Three Rivers Source Region in Qinghai Province, southeastern Tibet, western Sichuan, Qilian Mountains, southern Xinjiang and other parts of Western China, while there is one or no one found in coastal eastern China. In the past 15 years, the area proportion of high- quality ecosystems in 53% of the counties has increased. The vegetation coverage of counties in the Loess Plateau, Huang-Huai-Hai Plain, Beijing-Tianjin-Hebei region, Sichuan- Guizhou-Chongqing, and Guangdong and Guangxi provincial units has increased significantly. However, it has decreased in northern Xinjiang, central Tibet, central and eastern Inner Mongolia, Yangtze River Delta and other parts of China. The relationships between the numbers of ecological conservation programs and the indicators responding ecosystem restoration such as high- quality ecosystem and vegetation coverage do not show positive correlations. It is recommended that ecological conservation projects should be planned and implemented according to the distribution of high- quality ecosystems, and the restoration measures such as afforestation should follow natural principles and regional variations under the background of climate change.