It has been more than 10 years since the implementation of the planning strategy of National Key Ecological Function Zones. Therefore, it is of great significance to evaluate the ecological quality improvement effect of National Key Ecological Function Zones at the appropriate time, in order to promote the implementation and improvement of relevant ecological policies, which will also facilitate the development of Main Functional Area Planning. By constructing a theoretical framework for evaluating the effect of ecological quality improvement, and comprehensively applying the Driving force-Pressure-State-Impact-Response (abbreviated as DPSIR) model, the InVEST model and the obstacle degree model, we evaluated the ecological quality improvement level of the first batch of National Key Ecological Function Zones from 2010 to 2020 which cover 428 districts in total. And we zoned the study area on the basis of China’s terrestrial ecological base zones and with districts as the minimal evaluation unit. Furthermore, the obstacle degree model was utilized to identify the factors of ecological quality improvement in National Key Ecological Function Zones. The results showed that: (1) Generally speaking, the level of ecological quality enhancement in National Key Ecological Functional Zones from 2010 to 2020 was high, and the number of districts with the ecological quality enhancement level of "high" and "medium" was account for 86.45% of the total number of districts in National Key Ecological Functional Zones, which is a very large proportion of our study area. The order of ecological quality improvement level in the six ecological zones is as follows: Southeast Ecological Zones > Yangtze River and Sichuan-Yunnan Key Ecological Zones > Yellow River Key Ecological Zones > Northwest Ecological Zones > Tibetan Plateau Ecological Zones > Northeast Ecological Zones. (2) Particularly, the ecological environment quality and proportion of woodland or grassland in Hunshandake Desertification Control Ecological Functional Area, Northern Foothills of Yinshan Mountains Grassland Ecological Functional Area and Guangxi-Guizhou-Yunnan Karst Desertification Control Ecological Functional Area presented relatively significant improvement, while the night light index of Tarim River Desertification Control Ecological Functional Area and Three Gorges Reservoir Soil and Water Conservation Ecological Function Area showed an increasing trend, in the meantime, the vegetation cover and the net primary productivity decreases significantly, resulting in an increased pressure on ecosystems. (3) In terms of obstacle factors, the industrial development drive, wetland policy response, vegetation cover status, habitat function and the population carrying pressure are the main obstacles to ecological quality improvement in National Key Ecological Functional Zones. In conclusion, the results of the study can provide a reference basis for the construction of ecological environment quality in National Key Ecological Functional Zones.