The transfer payment to national key ecological function areas has become the largest ecological protection compensation project from the government level in China and even the world. The effect of its use of funds on local ecological and environmental protection particularly should be given more attention and stress. To solve the deficiencies of existing relevant research in research objects and data, this research was based on the multi-scale data that contains district and county data, provincial data, and the data from case city Shaanxi. By adopting the evaluation method of intuitive level value and its rate of change, statistical correlation test, and comparing counties which differ in batches of policies and types of ecological function zone, this research made a multi-dimensional assessment of the eco-environmental benefits of the transfer payment policy for national key ecological function areas, from the three aspects of natural ecological environment, atmospheric environment, and water environment. The research results showed that: (1) the ecological environment quality of counties that enjoy transfer payment was basically stable from 2011 to 2017, and some indicators of ecological characteristics showed a positive trend. Case analysis and provincial analysis showed that there was a significant positive correlation between transfer payment and wetland coverage. The transfer payment policy for key ecological function areas has played a positive role in stabilizing and improving the ecological quality of counties. (2) From 2015 to 2018, the average concentration of PM_2.5, SO₂, and NO₂ in the counties that enjoy transfer payment policy showed a downward trend, and the improvement of atmospheric environment was significant. Among them, the decrease of PM_2.5 concentration was particularly obvious and the decrease was the largest in counties in the wind-proof and sand-fixing ecological function areas. Relatively, the decrease of NO₂ concentration was small. Therefore, further efforts should be made to reduce the concentration of NO₂. (3) The indicators of water environment in counties given transfer payment fluctuated greatly from 2012 to 2018. Overall, the water environment quality generally improved slightly. The environmental quality of the counties which were added in 2016 showed a more significant improvement. The evaluation conclusions of this research showed that transfer payment to key national ecological function areas have had a positive impact on the county's ecological environment quality, with the most obvious improvement in the quality of atmospheric environment, while there is a room for further improvement in the improvement of ecology and water quality.