Regional carbon storage is a significant manifestation of ecosystem service functions. Examining the impact of changes in land use on carbon stock in the Chang-Zhu-Tan urban agglomeration under different topographic reliefs is paramount for sustainable land resource utilization and realizing carbon peaking and neutrality goals. Taking the Chang-Zhu-Tan Urban Agglomeration as an example, based on the InVEST model and combined with land use data to analyze the spatio-temporal variation of carbon storage, using the mean change point method to extract topographic relief. From the perspective of topographic relief, this study explores the correlation between changes in land use and carbon storage distribution patterns in the study area. The research results show that the optimal analysis window for topographic reliefs in the study area is 17×17, covering an area of 0.26 km2, with an average topographic relief of 78.58 m. From 2000 to 2020, changes in land use in the Chang-Zhu-Tan urban agglomeration primarily involved a gradual decrease in forest land, cultivated land, and grassland areas and a gradual increase in water and construction land. The carbon stock in the Chang-Zhu-Tan urban agglomeration showed a decreasing trend, with a total reduction of 13.37×106 tons over the past 20 years. The distribution of carbon stock across topographic reliefs mainly exhibits low-value and moderate-value carbon stock concentrations in flat and slightly undulating areas. In contrast, moderately high-value and high-value carbon stock concentrations are concentrated in gently and moderately undulating areas. These research findings provide a scientific foundation for optimizing the spatial pattern of the study area and formulating carbon peak and carbon-neutral policies.