Based on land use data from 1980, 1990, 2000, 2010, and 2020, the PLUS model was used to simulate land use changes in the Zoige Plateau by 2030 under three scenarios: natural development, ecological restoration, and economic development. The InVEST model was further employed to estimate the ecosystem carbon storage from 1980 to 2030. Finally, the Geographic Detector model was used to analyze the driving factors of spatial differentiation of carbon storage. The results showed that: (1) The major land use types in the Zoige Plateau were grassland, woodland, and wetland. From 1980 to 2020, the area of grassland in the region decreased, while the area of wetland and woodland increased. (2) The carbon storage of the Zoige Plateau ecosystem ranged from 1.240 billion tons to 1.291 billion tons from 1980 to 2020. Grassland and wetland were the main carbon storage ecosystem types in the Zoige Plateau. The areas with increased carbon storage over the last 40 years were mainly concentrated in the wetland areas of Zoige County, Maqu County, and Hongyuan County. (3) Carbon storage in 2030increased by 4.1443 million tons compared to 2020 under the ecological restoration scenario, decreased by 4.4567 million tons under natural development scenario, and decreased by 11.5958 million tons under economic development scenario. (4) The spatial differentiation of carbon storage in the Zoige Plateau ecosystem was primarily influenced by natural factors, of which elevation, annual mean temperature, soil type, and slope were all important drivers. Interaction detection indicates that the interaction between soil type and slope had the greatest impact.