[Objective] The ecosystem carbon storage and its response to land use changes in Fujian Province were analysed in order to provide a reference for ecosystem protection. [Methods] Based on land use data and carbon density data, the InVEST model was used to simulate carbon storage in Fujian Province in 1980, 2000, and 2020. The spatiotemporal characteristics of carbon storage and land use were analyzed using the distribution of cold spots and hot spots, transfer maps, and a transfer matrix. The response of carbon storage to land use changes was analyzed. [Results] (1) Carbon storage in Fujian Province was relatively high on the whole, and more than 82.5% of the region was above medium carbon storage (＞3000 t), mainly located in mountainous and hilly areas, which were also hot spots of high carbon storage. Ares of high (hot spots) and low (cold spots) of carbon storage concentration transferred less. Total carbon storage fluctuated slightly from 1980 to 2020, and relatively more carbon storage transferred between different carbon storage levels from 2000 to 2020. (2) Land use/cover in Fujian Province was mainly forest land (61.4%–62.9%), followed by cultivated land (16.9%–18.3%) and grassland (15.2%–17.2%). Land use/cover change was relatively stable from 1980 to 2000, and more intense from 2000 to 2020. (3) Total carbon storage values in forest land, grassland, and cultivated land were relatively high, while total carbon storage in water bodies, construction land, and unused land were relatively low. Total carbon storage in cultivated land decreased over time, while total carbon storage of construction land increased. The area of forest land and grassland both increased and decreased. The largest transfer of total carbon storage caused by land use/cover changes was observed in forest land, followed by grassland and cultivated land. The net transfer of total carbon storage was negative for forest land, and positive for the other land use classes. The largest carbon loss was observed for the transfer of forest land. [Conclusion] Cultivated land, forest land, and grassland were the main types of land use in Fujian Province contributing to higher carbon storage, and their mutual transfer resulted in carbon storage changes.