[Objective] The effects of land use change on the evolution of habitat quality and carbon storage in the Wuding River basin and their future trends were analyzed in order to provide data support for land use planning and sustainable ecological development in this region. [Methods] Land use changes in 2033 were predicted using the PLUS model. The InVEST model was then used to evaluate habitat quality and carbon storage in the river basin from 2003 to 2033, and spatial autocorrelation analysis was conducted to reveal their spatial clustering characteristics. [Results] From 2003 to 2023, land use in the Wuding River basin was dominated by grassland and cultivated land, accounting for 74.36%—78.40% and 14.03%—15.20%, respectively. The areas of cultivated land, forest land and construction land all increased annually, and the mutual conversion between cultivated land and grassland, and the conversion from bare land to grassland were the main land use transition types. Habitat quality and carbon storage showed increasing trends year by year, with an overall spatial pattern of low values in the central area and high values on the periphery. Areas with high habitat quality were mainly distributed in forest land, grassland and water bodies, whereas areas with high carbon storage were mainly distributed in grassland and cultivated land. The spatial clustering pattern of habitat quality consistently showed a ring-shaped distribution, whereas carbon density changed significantly from an early ring-shaped distribution to a later pattern characterized by low-low clustering in the central area and high-high clustering in the southern area. This divergence indicated that ecological engineering effectively changed the spatial heterogeneity of carbon density within the bare land, but did not reverse the habitat quality pattern primarily controlled by the distance to stress factors. In addition, cultivated areas in the central and southern parts of the river basin showed low-low clustering of habitat quality but no significant clustering of carbon storage, highlighting the trade-off between the two ecosystem service functions under agricultural activities. [Conclusion] It is recommended to delineate protection boundaries for forest land and grassland, prevent the encroachment of cultivated land and construction land, establish plant communities with greater carbon sequestration potential in bare land areas, moderately explore industries such as photovoltaic power generation, and control the expansion boundary of construction land, so as to promote ecosystem stability and improvement in the Wuding River basin.