Exploring the spatial-temporal changes, driving forces, and future development tendency of the carbon sequestration service function of the Three-River-Source National Park ecosystem has great significance for regional ecological protection and sustainable development. Historical land-use data of Three-River-Source National Park from 1990 to 2020 were selected at five-year intervals, and based on the PLUS-InVEST-Geodector model, the spatial-temporal changes of historical carbon storage were analyzed, and the driving forces of spatial-temporal variation were explored combined with multiple factors. The carbon storage of Three-River-Source National Park in 2030 was predicted under the scenarios of natural development and ecological protection. The results showed that: ① The carbon storage of Three-River-Source National Park showed a fluctuating characteristic of increase-decrease-increase-decrease from 1990 to 2020, the carbon storage was increased by 41.85×106 t overall, and the grassland took the largest contribution. ② The spatial distribution characteristics of carbon storage in Three-River-Source National Park had little change between 1990 to 2020, and the evolution of the spatial distribution was relatively stable. The contribution ratio of the Yangtze River source park, Lancang River source park, and Yellow River source park was 7∶1∶2, which was roughly equivalent to the park area. ③ The major driving factors of the spatial-temporal variation of carbon storage in Three-River-Source National Park from 1990 to 2020 were: FVC, soil type, and annual precipitation. The interactive detection of each driving factor showed dual-factor enhancement and nonlinear enhancement. ④ The carbon storage of Three-River-Source National Park was predicted to decrease by 4.87% and 3.98% from 2020 to 2030 under the scenarios of natural development and ecological protection, respectively, and the carbon storage reduction under the ecological protection scenario had a significant inhibitory effect. The findings can provide data support for national spatial planning of Three-River-Source National Park and the enhancement of terrestrial ecosystem carbon storage.