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National land spatial planning is dominated by urban-agricultural-ecological functions and has become a Chinese national strategic issue. However, the three functional spaces have serious conflicts in the karst areas, causing inconsistencies in regional development and triggering poverty and a more serious situation for the ecological environment. In this study, we used the gray multi-objective dynamic programming model and the conversion of land use and its effects at small region extent model to simulate the developmental structures of future land use in the karst areas of Southwest China under a socioeconomic development scenario, an arable land protection scenario and an ecological security scenario. Finally, based on the coordination of the urban-agricultural-ecological functions, we used a functional space classification method to optimize the spatial structures of the national land space for 2035 year and to identify different functional areas. The results showed that the three scenarios with different objectives had differences in the quantities and spatial structures of land use but that the area of forestland was the largest and the area of water was the smallest in each scenario. The optimization of the national land space was divided into seven functional areas—urban space, agricultural space, ecological space, urban-agricultural space, urban-ecological space, agricultural-ecological space and urban-agricultural-ecological space. The ecological space was the largest and the urban-ecological space was the smallest among seven functional areas. The different types of functional spaces had significant differentiation characteristics in the layouts. The urban-agricultural space, urban-ecological space, agricultural-ecological space and urban-agricultural-ecological space can effectively alleviate the impacts of human activities and agricultural production activities in karst areas, promote the improvement of rocky desertification and improve the quality of the regional ecological environment. The results of this research can provide support for decisions about the balanced development of the national land space and the improvement of environmental quality in the karst areas.

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