Cultivation of Caragana liouana, which is also known as planted shrub encroachment, has greatly changed the vegetation structure and carbon cycles of regional ecosystem in Yanchi County since 1970. However, there are insufficient studies to quantitatively evaluate the effects of this anthropogenic measurement on carbon storage in the desert steppe ecosystem. Meanwhile, the work to understand the effects of planted shrub encroachment on carbon storage of desert steppe ecosystem not only expose the feedback mechanism of carbon cycle on the anthropogenic activity but also provide a scientific basis for local government on the ecological restoration project. In this study, we combined Biome-BGC and Logistics growth model to simulate the carbon storage dynamics in desert steppe before and after planting shrub during 1958-2017, and quantitatively analyzed the effects of the planted shrub encroachment on 4 kinds of carbon storage in the ecosystem. The results are as follows:(1) combination of Biome-BGC and Logistics growth model could accurately simulate the carbon storage dynamic changes during the process of the planted shrub encroachment in the desert steppe ecosystem. (2) Characteristics of carbon storage accumulation were changed a lot by planting shrubbery. Rapid growth stages of Caragana liouana greatly enhanced the total carbon storage of desert steppe ecosystem, while led to the transformation from grassland to shrub ecosystem. (3) The planted shrub encroachment changed the ratio of various types carbon in total carbon storage, especially affected vegetation and litter carbon storage, which significantly increased by 6 times and 1.76 times, respectively, while the soil carbon storage has not changed clearly in the short term, because the conversion process of vegetation carbon to soil carbon was slow. These results indicated that the planted shrub encroachment could significantly enhance the carbon sequestration capacity of the desert steppe ecosystem, and provide a feasible path to carbon neutrality and addressing climate change.