National Key Ecological Function Areas (NKEFA) are important areas to ensure national ecological security and improve the quality of the ecological environment. This study compared the ecological environmental quality changes combined with land use transitions of NKEFA and non-NKEFA in 2000 and 2010 to form a comprehensive understanding of the quality of the ecological environment in NKEFA before the implementation of the transfer payment policy. The results indicated that the land cover types of NKEFA and non-NKEFA were both dominated by ecological land and the proportion of ecological land decreased between 2000 and 2010. In addition, the proportion of ecological land of NKEFA was higher than that of non-NKEFA both in 2000 and 2010 and the degree of conversion of land cover types was smaller in NKEFA than that of non-NKEFA. The vegetation coverage, biomass, and net primary productivity (NPP) of NKEFA and non-NKEFA both gradually decreased from southeast to northwest. According to the types of ecological function areas, the vegetation coverage was highest in the soil and water conservation function areas, and the average biomass density and average NPP were highest in the biodiversity maintenance function areas, and the total biomass and total NPP of water conservation function areas were the highest. Windbreak and sand-fixation function areas were mainly located in the northwest inland, leading to the lowest vegetation coverage, biomass density, and total biomass, average NPP and total NPP. Overall, the ecosystem quality of NKEFA improved from 2000 to 2010. However, the degree of improvement was not as large as that of non-NKEFA. This suggests that implementing ecological protection engineering projects and transfer payments policy can further improve the environment quality of NKEFA and plays an important role in enhancing the level of ecological security of the entire country.