Evaluation of the environmental air quality in counties of the national key ecological function areas is of practical significance to the implementation of the ecological civilization construction and transfer payment system for the national key ecological function areas. Took the air quality of transfer payment counties in the national key ecological function areas as the evaluation object, the status and changes of ambient air quality were evaluated and analyzed based on the daily average data of air quality monitoring stations from 2015 to 2019. The conclusion of the research indicated that the overall air quality of transfer payment counties in the national key ecological function areas was generally good and improving, transfer payment policy has a significant promoting effect on the improvement of air quality in the national key functional areas from 2015 to 2019. The proportion of counties with more than 90% good air quality days increased from 33.77% in 2015 to 69.52% in 2019, and the water conservation areas` proportion of excellent air quality days increased from 72.71% in 2015 to 92.09% in 2019, with the most significant improvement in air quality. Between 2015 and 2019, with the significantly decreased in proportion of fine particulate matter (PM_2.5) pollution, and increased in the proportion of ozone (O₃) pollution, the main non-attainment pollutants were gradually changed from particulate matter to particulate matter and ozone. At present inhalable particles (PM₁₀) and fine particulate matter were the main over standard pollutants in the sand fixation areas, and fine particulate matter and ozone were the other three types of the national key ecological function areas. There were significant spatial differences in air quality in the national key ecological function areas, and air pollution exhibited significant spatial aggregation characteristics. Among the four ecological function areas, the air quality of the biodiversity conservation areas was the best, followed by the water conservation areas, the water and soil conservation areas was slightly worse, and the sand fixation areas was the worst. The national key ecological function areas undertake the important function of guaranteeing national ecological safety. In the future, it is still necessary to continue to strengthen the air quality monitoring of the national key ecological function areas and refine the evaluation index system of ecosystem construction, so as to provide a scientific basis for the effective implementation of ecological environment protection measures and the management decision-making of ecological environment construction of the national key ecological functional areas.