Desert steppe ecosystems are sensitive to climate change. How does the carbon cycle respond to climate change is still ambiguous. This study simulated the carbon dynamic of desert steppe ecosystems in four kinds of climate scenarios using the Biome-Bio Geochemical Cycles (Biome-BGC) model based on meteorological data set from 1958 to 2017 in Yanchi county, Ningxia province. The results indicated that the average annually total carbon storage of desert steppe ecosystem ranged from 2.3208 kg/m² to 2.3652 kg/m² in the four climate scenarios. The soil carbon storage accounts for 94.03% of the total carbon storage. The litter and vegetation carbon storage account for 4.03% and 1.94% of the total carbon storage, respectively. In the past 60 years, the soil carbon storage in the benchmark scenario, which means in the scenario without climate change, accumulated at the rate of 0.0020 kg/m² per year while the total carbon storage presented a rising trend in fluctuation. The annual change of vegetation and litter carbon storage were closely related to the change of seasons. The soil carbon storage was lowest in summer and autumn over the whole year. The increasing temperature resulted in the minor decrease of a variety of carbon storage, whereas, the increasing of precipitation led to the significant rise of these carbon storages. Therefore, the combination of temperature and precipitation explains the increment of carbon storage in climate change. In addition, the litter carbon storage is the most sensitive kind of carbon to climate change, followed by vegetation carbon storage and soil carbon storage. The results revealed the changing laws of carbon storage in desert steppe ecosystem in various climate scenarios. These can provide scientific basis for local governments to adopt proper strategies for adapting climate change and to make policies for the ecological restoration.