Vegetation carbon sequestration in alpine areas of West China, such as the Qilian Mountains on the northeastern Tibetan Plateau, has been subject to long-term human intervention under a warming climate since the launch of the western development strategy (WDS) in 2000. However, the human impacts on vegetation carbon sequestration capacity during this period remain unclear. In this study, the magnitude and direction of human impacts on vegetation carbon sequestration capacity (defined as net primary production, NPP) were assessed by the deviation of remote-sensing–estimated actual NPP data from the simulated potential NPP. The potential value was derived from natural system coupling under the assumption that human activities ceased during the assessment period. The impacts of natural forces and historic human activities were then effectively exfoliated in our final assessment using a process-based IBISi model. The results indicate that the total actual vegetation carbon sequestration capacity in the Qilian Mountains has reduced compared with its potential value since the WDS launched. This reduction was mainly attributed to grazing in the grasslands. However, deforestation, mineral resource exploitation, and the construction of hydropower facilities have also caused a reduction in vegetation carbon sequestration capacity at the local scales. In contrast, forestry protections and afforestation, and agricultural activities associated with reclamation, cultivation, irrigation, and fertilization, have resulted in local increases in the vegetation carbon sequestration capacity in the corresponding forest lands, shrublands, and croplands. These findings highlight the importance of ecological protections for vegetation carbon sequestration and were expected to provide evidence to verify the improvement of ecological management and the increasing of carbon sinks in West China.