The national key ecological function zones are important national ecological security barriers, and their ecological protection value is of great significance for maintaining national ecological security. The policy of financial transfer payment was established to protect ecosystems and environment in those zones. In order to evaluate the ecological effects of financial transfer payment policy, 25 national key ecological functional areas and their four types of natural functional zonings are used as research areas in this paper. Based on the value equivalent factor of unit area value, the ecosystem service values and their change in 2010-2015 were quantitatively estimated by using the methods of model operation and geographic information spatial analysis. The results showed that (1) in 2015, the value of ecosystem services in key functional areas of the country presented an obvious distribution pattern of "low in northwest and high in southeast". From the perspective of 25 key ecological function areas, the area of the medium-high value area accounts for 31.60% and the number accounts for 60%. The ecosystem service value of the four types of natural ecological functional areas from the highest to the lowest is the soil and water conservation type functional area, the biodiversity maintenance type functional area, the water source conservation type functional area, and the wind and sand fixation type functional area. (2) From 2010 to 2015, the value of ecosystem services in key national ecological functional areas showed a significant increase, with an increase of 16.46%. In terms of the spatial distribution, the ecosystem service value of 80.14% of the key eco-functional areas remained basically unchanged. According to the characteristics of grading change, the area of the high value area increases, the area of the median area decreases, and the area of the low value area decreases. (3) In the past five years, there have been 21 increases in the value of ecosystem services in 25 key ecological areas, accounting for 84.00%. However, the range of changes in the areas where ecosystem service value decreased was less than 1.00%. The ecosystem service value of the four types of natural ecological function areas showed an increasing trend, and the change ranged from high to low were soil and water conservation ecological function area (1.44%), water conservation ecological function area (0.22%), wind prevention and sand fixation ecological function area (0.21%), and biodiversity ecological function area (0.08%). The value level of ecosystem services is on the rise as a whole, which reflects the obvious effect of ecological protection and engineering construction. The research results can not only provide a scientific basis for the quantitative and comprehensive assessment of ecosystem protection, improvement and its effects, but also provide an effective reference for the construction of important ecological functional areas and the construction of national ecological security patterns.