Understanding the impact mechanisms of territorial space composition and landscape pattern changes on carbon storage is critical to balance the development and utilization of territorial space and the conservation of the ecosystem. Thus, taking the Fujian Delta urban agglomeration (FDUA) of China as an example, this paper analyzed the impact of the transference in territorial space composition and the change in the coupling coordination degree (CCD) of landscape patterns on carbon storage based on the urban-rural gradient and grid scales. Results illustrated that the areas of agricultural, green, and blue spaces continued to decline, while the intensity of economic space expansion increased from 20.86 to 42.45% during 2000-2020. The grids with CCD change of landscape patterns declined mainly (accounting for 64.31%) in the first decade and rose mainly (accounting for 76.79%) in the second decade. The carbon loss of each under rural gradient was gradually serious. The percentage of grids with moderate and significant decrease in carbon storage escalated from 27.83 to 70.21%. Additionally, grids experiencing high carbon loss moved from the northeast coast to the southwest inland. The response of carbon storage change showed that the expansion of agricultural space occupied by economic space played a crucial role in the carbon loss in each urban-rural gradient. The carbon loss caused by supplementing agricultural space with green space increased from the urban to the field. Enhancing the CCD of landscape patterns can boost carbon storage, and the scattering expansion of economic space needs to be avoided. This paper provides a novel perspective to explore the spatial response of carbon storage change to the territorial space composition and landscape pattern evolution, which is important to optimize the territorial space pattern and improve the regional carbon sink capacity.