The spatial–temporal distribution and evolution characteristics of carbon stock under the influence of land use changes are crucial to the scientific management of environmental resources and the optimization of land spatial layout. Taking the Xiamen–Zhangzhou–Quanzhou urban agglomeration in the southeastern coastal region of China as an example, based on seven land use types from 1990 to 2020, including cultivated land, woodland, and construction land, we quantitatively investigate the spatial–temporal patterns of carbon stock development and the spatial correlation of carbon stock distribution. Additionally, two scenarios for the development of urban and ecological priorities in 2060 are established to investigate the effects of land use changes on carbon stock. The results indicate that (1) the research area has formed a land use spatial pattern centered around urban construction in the eastern bay area, with the western forest area and coastal forest belt serving as ecological barriers. Carbon stock is influenced by land use type, and the distribution of total carbon stock exhibits a spatial aggregation phenomenon characterized by “low in the southeast, high in the north, and medium in the center”. (2) Distance of trunk and secondary roads, elevation, slope, watershed borders, population size, and gross domestic product (GDP) factors are the main drivers of the growth of land use types. The primary causes of the reduction in carbon stock are the widespread conversion of cultivated land, woodland, and grassland into construction land, as well as water and unused land. (3) In 2060, there will be a decrease of 41,712,443.35 Mg in the urban priority development scenario compared to 2020, and a decrease of 29,577,580.48 Mg in the ecological priority development scenario. The estimated carbon stock under the two scenarios varies by 12,134,862.88 Mg. The average carbon storage of Zhangpu County, Quangang County, and Jimei County is expected to rise by one level under the ecological protection scenario, indicating that the vast forest area can become a potential area to maintain carbon stock. It is crucial to encourage the coordinated development of peri-urban agroforestry and ecological barriers, as well as to establish a harmonious spatial pattern of land use and carbon stock at the scale of urban agglomerations.