The natural ecological lands, such as forest land, grassland, wetland, etc., constitute the most important factor for maintaining and preserving the earth’s ecosystem, which must be well concerned in the regional function-oriented planning for the sustainability of human economic development. We analyzed and evaluated the change of natural ecological land in the function-oriented planning regions where we applied the major function-oriented zones introduced as a new concept in China. Using the land-use data from 2009 to 2018 that were produced by the National Land Use Survey, we re-classified natural ecological land types into the forest, grassland, wetland, and bare land, and then addressed the changes of natural ecological land types from 2009 to 2018 in the major function-oriented zones. As a result, the area of natural ecological lands generally tended to decrease from 2009 to 2018, while the decreasing trend of natural ecological land areas was controlled after 2015 with the implementation of governmental policies for environment protection and eco-logical projects. Especially, the decrease of forest land area significantly tended to be zero in 2018 in optimal development zones. The decreased areas of natural ecological lands were mostly converted from artificial land from 2008 to 2019. On the other side, the forest lands mostly changed from cropland and grassland in key development zones, agricultural production zones, and key ecological function zones, due to the fact that grassland conversed in afforestation during this period. The evaluation of natural ecological land changes, which could be implemented by using the annual updates of national land-use data in China, is significant to support the government’s spatial regulation design, to reshape the planned regions, and make policies for environmental restoration and protection management.