Abstract: Habitat quality reflects the ecological status of a region, serving as the foundation for all ecosystem services and functions, and is crucial for formulating policies on regional ecological protection and land use planning. The peak cluster depression basin in southwest Guangxi is a vital ecological barrier within the Pearl River basin, and it is also a significant area for water conservation and biodiversity protection in China. This study utilizes land use data and driving factors from 2000, 2010, and 2020. The CA Markov model is employed to simulate and predict land use for 2030 under three scenarios: natural development, food security, and ecological protection. Subsequently, the InVEST model is used to assess habitat quality across these scenarios from 2000 to 2030. The findings reveal that: (1) The average habitat quality indices for 2000, 2010, and 2020 were 0.776, 0.785, and 0.793 respectively, indicating a generally high level of habitat quality. (2) For 2030, the average habitat quality indices under the natural development, food security, and ecological protection scenarios would be 0.798, 0.779, and 0.807 respectively. The ecological protection scenario showed the greatest increase in high-quality habitat area, followed by the natural development scenario. The high-quality habitat area under the food security scenario will be lower than in 2020, and even lower than in 2010. (3) Land use type was the primary factor influencing habitat quality spatial variation in the peaked depression watersheds of southwestern Guangxi, followed by NDVI, elevation, slope, and the degree of rocky desertification. The combined explanatory power of the climatic environment was relatively minor. To enhance the ecological environment in Karst Plateau areas, it is imperative to strictly enforce the protection boundaries defined in land use planning, reasonably control the development scale of construction land, optimize the ecological compensation mechanisms, and implement ecological restoration policies such as Grain for Green and grassland restoration.