The main causes of habitat conversion, degradation, and fragmentation—all of which add to the loss in biodiversity—are human activities, such as urbanization and farmland reclamation. In order to inform scientific land management and biodiversity conservation strategies and, therefore, advance sustainable development, it is imperative to evaluate the effects of land-use changes on biodiversity, especially in areas with high biodiversity. Using data from five future land-use scenarios under various Shared Socioeconomic Pathways (SSPs) and Representative Concentration Pathways (RCPs), this study systematically assesses the characteristics of land-use and landscape pattern changes in southwest China by 2050. This study builds a comprehensive biodiversity index and forecasts trends in species richness and habitat quality using models like Fragstats and InVEST to evaluate the overall effects of future land-use changes on biodiversity. The research yielded the subsequent conclusions: (1) Grasslands and woods will continue to be the primary land uses in southwest China in the future. But the amount of grassland is expected to decrease by 11,521 to 102,832 km2, and the amounts of wasteland and urban area are expected to increase by 8130 to 16,293 km2 and 4028 to 19,677 km2, respectively. Furthermore, it is anticipated that metropolitan areas will see an increase in landscape fragmentation and shape complexity, whereas forests and wastelands will see a decrease in these aspects. (2) In southwest China, there is a synergistic relationship between species richness and habitat quality, and both are still at relatively high levels. In terms of species richness and habitat quality, the percentage of regions categorized as outstanding and good range from 71.63% to 74.33% and 70.13% to 75.83%, respectively. The environmental circumstances for species survival and habitat quality are expected to worsen in comparison to 2020, notwithstanding these high levels. Western Sichuan, southern Guizhou, and western Yunnan are home to most of the high-habitat-quality and species-richness areas, while the western plateau is home to the majority of the lower scoring areas. (3) The majority of areas (89.84% to 94.29%) are forecast to undergo little change in the spatial distribution of biodiversity in southwest China, and the general quality of the ecological environment is predicted to stay favorable. Except in the SSP1-RCP2.6 scenario, however, it is expected that the region with declining biodiversity will exceed those with increasing biodiversity. In comparison to 2020, there is a projected decline of 1.0562% to 5.2491% in the comprehensive biodiversity index. These results underscore the major obstacles to the conservation of biodiversity in the area, highlighting the need to fortify macro-level land-use management, put into practice efficient regional conservation plans, and incorporate traditional knowledge in order to save biodiversity.