Land use/cover change (LUCC) has an important impact on the terrestrial carbon cycle. The spatial distribution of regional carbon reserves can provide the scientific basis for the management of ecosystem carbon storage and the formulation of ecological and environmental policies. This paper proposes a method combining the CA-based FLUS model and the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model to assess the temporal and spatial changes in ecosystem carbon storage due to land-use changes over 1990–2015 in the Qinghai Lake Basin (QLB). Furthermore, future ecosystem carbon storage is simulated and evaluated over 2020–2030 under three scenarios of natural growth (NG), cropland protection (CP), and ecological protection (EP). The long-term spatial variations in carbon storage in the QLB are discussed. The results show that: (1) Carbon storage in the QLB decreased at first (1990–2000) and increased later (2000–2010), with total carbon storage increasing by 1.60 Tg C (Teragram: a unit of mass equal to 10¹² g). From 2010 to 2015, carbon storage displayed a downward trend, with a sharp decrease in wetlands and croplands as the main cause; (2) Under the NG scenario, carbon reserves decrease by 0.69 Tg C over 2020–2030. These reserves increase significantly by 6.77 Tg C and 7.54 Tg C under the CP and EP scenarios, respectively, thus promoting the benign development of the regional ecological environment. This study improves our understanding on the impact of land-use change on carbon storage for the QLB in the northeastern Qinghai–Tibetan Plateau (QTP).