To explore the impact of land-use change on carbon storage, this study coupled the InVEST model and the FLUS model to analyse the spatial and temporal characteristics of carbon storage in the Qiantang River source region from 2000 to 2030. The carbon storage in the study area is evaluated which declined rapidly from 166.22 × 106 t in 2000 to 164.41 × 106 t in 2020, and the spatial distribution of carbon storage could be characterized by “the northwest and the southwest of region with higher, the east and the centre of the region with lower”. The carbon storage was simulated based on the historical trend development scenario, the food security scenario, and the ecological protection scenario. The carbon storage with the food security scenario could achieve 162.74 × 106 t in 2030. The carbon storage with the ecological protection scenario had an increase of 62.60 t/km2 compared to the historical natural tendency development. Interestingly, the food security scenario had the smallest carbon loss value which is about $1.39 × 109, and its net carbon storage value was the largest which is about $3.71 × 109. The results of this study could provide a scientific reference for the conservation of carbon storage and land use management for climate change and sustainable development. This paper also can lay the foundation for subsequent further studies such as artificial intelligence.