Carbon sequestration is among the main functions of terrestrial ecosystem services, and the carbon sequestration capacity of terrestrial ecosystems directly affects global carbon emissions and climate change processes. Human activities directly influence land use and cover change, consequently affecting the carbon sequestration function of ecosystems. The terrestrial ecosystem services in dry and cold regions are more vulnerable and significantly impacted by human activities. Therefore, utilizing land use data from the Irtysh River Basin in the Altai Mountains from 2000 to 2020, the InVEST model was used to estimate and analyze the spatial distribution of carbon stocks in the basin during different periods. Subsequently, the influence of human activities on the spatial distribution of carbon stocks was discussed. The results show the following: (1) The main land use types in the basin are woodland, grassland, and unused land, and the land use pattern changed significantly from 2000 to 2020. Cultivated land, urban and rural land, industrial and mining land, and residential land expanded continuously, increasing by 2619.35 km2 and 186.68 km2, respectively. Grassland and water areas initially decreased and then expanded, increasing by 4725.13 km2 and 33.47 km2, respectively. Meanwhile, forest land and unused land decreased continuously by 2328.88 km2 and 5237.76 km2, respectively. (2) During this period, the spatial distribution pattern of carbon stocks in the basin was similar and showed a zonal distribution. High-value areas were distributed in high-altitude regions where grassland and woodland were clustered, while low-value areas were distributed in low-altitude regions where unused land was clustered. In 2000, 2005, 2010, 2015, 2020 the total carbon storage in the basin was 641.60 Tg, 645.78 Tg, 646.83 Tg, 650.28 Tg, and 665.91 Tg, respectively, with an annual growth rate of 0.95%, showing an upward trend. (3) The areas in the basin where carbon storage decreased or increased showed a spot-like distribution. Furthermore, carbon storage reduction mainly occurred through the conversion of grassland to unused land and cultivated land, with an average annual reduction of 58.81 Tg. The increase in carbon storage primarily resulted from the conversion of unused land into cultivated land and grassland, with an average annual increase of 64.82 Tg. From 2000 to 2020, the net sequestration of carbon storage exceeded the net release, indicating an increasing carbon sequestration capacity in the Irtysh River Basin. Overall, the reclamation of land and grass due to human activities is the main reason for the increase in carbon storage in the basin. However, it is necessary to coordinate the development and utilization of water and soil resources, as this will guarantee not only an increased carbon sink but also the preservation of the carrying capacity of water and soil resources, ultimately achieving sustainable economic development in the Irtysh River Basin. The results of this study will help to promote the carbon cycle of the basin and the carbon sequestration capacity of the ecosystem, as well as provide a scientific basis for the establishment and management of the basin carbon pool.