The inorganic carbon sequestration capacity of deserts in an arid region is now still questioned for their accuracy. The key question is whether the result of CO2 absorption from aboveground flux observation can be reflected in the soil carbon pool or not. In the arid region of northwest China, desert is divided into three types based on the landscape and vegetation characteristics, namely gravel desert (Gobi), sand desert, and silt desert. By measuring and analyzing the soil particle composition, total salt content, organic carbon and inorganic carbon content, the changes in soil organic carbon (SOC) and soil inorganic carbon (SIC) density and their storage in different type deserts were studied, and then they were compared with that in the alpine ecosystem of southwest China. The results showed that the average SIC densities in 0–30 cm surface soil layer and 1 m soil depth in different type deserts were 2.8 and 10.1 kg C m−2, respectively. Comparatively, the SIC density of silt desert was the highest, and the value over 12 kg C m−2 in 1 m soil depth. In our study, the average total carbon densities in 0–30 cm desert soil layer was 3.5 kg C m−2, and in 1 m soil depth was 12.1 kg C m−2. According to the value of 100 g C m−2 a−1 to calculate, the carbon accumulation in 0–30 cm surface soil layer and 1 m soil depth need 35 years and 121 years, respectively. If the value is less than 100 g C m−2 a−1, a longer period is required, showed that it will take a long time for the formation of desert inorganic carbon pool. In terms of material content, the average bulk density in 1 m soil depth was 1.52 g cm−3, and the total carbon accumulated in desert soil accounted for 0.8% of soil mass in 121 years, of which the inorganic carbon accounted for 0.7% of soil mass. For the soil absorption and inorganic sequestration to CO2, we proposed the concept of soil carbon assimilation. Carbon sequestration in desert ecosystems is plant carbon assimilation and soil carbon assimilation, which is a combination of organic and inorganic processes. The SIC density and storage of desert soil are five times that of SOC. The pathway of soil carbon assimilation can be divided into three stages: the reaction stage between CO2 and H2O, the reaction stage between CO2 or weak carbonic acid and soil solution cation, and the stage that is the dissolved and precipitated carbonates which attached to soil particles and downward deposition. The soil carbon assimilation capacity was enhanced by increasing the soil organic carbon, salt content, water content, and soil silt and clay content. To recovering and conservation of desert vegetation, the desert is reclaimed into farmland under the carrying capacity of water resources, the SOC density was not only increased, the soil carbon assimilation capacity, SIC density and storage are also enhanced greatly. Under conditions of future climatic warming, soil inorganic carbon sequestration capacity will be increased and carbon sequestration capacity of the desert ecosystem will be enhanced with increasing precipitation in the arid region. The development of irrigated agriculture in the arid desert region will be beneficial to a collaborative improvement in production and ecological functions in the arid region.