In recent years, the “dual carbon” issue has become a major focus of the international community. Changes in land use driven by anthropogenic activities have a profound impact on ecosystem structure and carbon cycling. This study quantitatively assesses the spatiotemporal changes in cropland occupation and supplementation in the Pearl River Delta from 2000 to 2020 using the InVEST model, analyzing the spatial clustering of carbon storage changes caused by variations in cropland area. The PLUS model was employed to simulate land-use patterns and the spatial distribution of carbon storage in four future development scenarios. The results indicate the following: (1) From 2000 to 2020, the net change rate of cropland area in the Pearl River Delta was −0.81%, with a decrease of 16.49 km2 in cropland area, primarily converted to built-up land and forest land. (2) Carbon storage in the Pearl River Delta exhibited a pattern of lower values in the center and higher values in the periphery. The terrestrial ecosystem carbon storage in the Pearl River Delta was 534.62 × 106 t in 2000, 518.60 × 106 t in 2010, and 512.57 × 106 t in 2020, showing an overall decreasing trend. The conversion of cropland and forest land was the main reason for the decline in total regional carbon storage. (3) The area of carbon sequestration lost due to cropland occupation was significantly greater than the area of carbon loss compensated by new cropland, indicating an imbalance in the quality of cropland occupation and supplementation as a crucial factor contributing to regional carbon loss. (4) Under the ecological priority scenario, the expansion of built-up land and the reduction in ecological land such as cropland and forest land were effectively controlled, resulting in the minimal loss of carbon storage. The soil organic carbon pool of cropland is the most active carbon pool in terrestrial ecosystems and has a significant impact on carbon storage. Clarifying the relationship between “cropland protection measures–land use changes–ecosystem carbon storage” will improve cropland protection policies, provide references for regional carbon sequestration enhancement, and support sustainable socio-economic development.
