This study aims to analyze the spatiotemporal land-use patterns in the forest-farmland ecotone of ecologically sensitive areas, together with their effects on carbon storage. Effective approaches were proposed to enhance carbon sequestration. The PLUS-InVEST model was also utilized along with the Geodetector. A systematic investigation was implemented to assess the impacts of spatiotemporal land-use patterns from 1990 to 2030 on the carbon storage of terrestrial ecosystems in the forest-farmland ecotone of the Greater Khingan Mountains. Additionally, the driving factors were determined responsible for the changes in carbon storage. The results were summarized as follows:1) The land-use types that experienced the largest area of transition were forests, grasslands, and croplands between 1990 and 2020. Notably, the highest conversion rates were observed in bare land (75.00%), water bodies (61.33%), and impervious surfaces (61.15%). The forest and grassland areas were expected to significantly increase under natural conservation and ecological protection scenarios by 2030. Furthermore, the areas of cropland and grassland were projected to increase under the cropland protection scenario, while the forest areas decreased greatly. The area of cropland declined in the urban development scenario, due to the urban expansion and land-use changes. 2) The total carbon storage in the study area exhibited a general downward trend, decreasing by 6.08×10⁷ t over the past two decades. The largest decrease in carbon storage occurred in forests, followed by grasslands and croplands. In contrast, there was the increasing carbon storage in the impervious surfaces. The carbon storage in 2020 was compared to the projections for 2030. The total carbon storage for 2030 was projected as 1.555×10⁹, 1.562×10⁹, 1.562×10⁹, and 1.561×10⁹ t, respectively, under the four scenarios of cultivated land protection, natural development, ecological protection, urban development, respectively. All scenarios indicated an increase in the total carbon storage, except for the cropland protection. Different scenarios of land-use management varied greatly in the potential of overall carbon sequestration at regional. Natural conservation and ecological protection share the most promise to increase carbon storage. 3) The elevation, population density, and slope were identified as the primary driving factors behind the spatial differentiation of carbon storage in the study area. Among them, there was the most significant interaction between slope and population density, with an interaction strength of 0.74. There was a much stronger impact of multiple driving factors on carbon storage, compared with any single factor. Multi-factorial approaches were also required to analyze the spatial dynamics of carbon storage. Therefore, the carbon dynamics of the ecosystem depended mainly on the land-use transitions in the ecotonal regions, like forest-farmland interfaces. The important implications were gained to develop the data-driven strategies of land management. Carbon sinks were also optimized to support biodiversity conservation. Overall, the significant role of targeted interventions was highlighted for the land-use changes in carbon storage and sequestration at regional scales. The findings can greatly contribute to ecosystem management and climate adaptation in the Greater Khingan Mountains.