Ecological function reflects the ability of the land to provide ecological goods to support high-quality human production and life. The evaluation of the county-level ecological function across the whole nation is crucial for sustainable land management, which has not been implemented effectively in China. In this study, we proposed a unified system for the assessment of ecological function that would be comparable at the county level, and we applied the system to evaluate the ecological function of 2850 counties across China based on multi-source data. We also examined the spatiotemporal changes in ecological function from 2009 to 2015 using standard deviational ellipses and coefficients of variation. The results showed that the number of counties with high levels of ecological function in China decreased by 8.13% from 2009 to 2012 and then increased by 0.6% from 2012 to 2015. The spatial pattern of the degradation of ecological function shifted from the east-west direction to the southwest-northeast direction and became centralized in the Central Plains area of China. The regional imbalance in ecological function followed the order from high to low of the central, western, northeastern, and eastern areas of China. Targeted policies were proposed to control the degradation of the ecological function in the four regions in China.