Soil organic carbon (SOC) and soil inorganic carbon (SIC) are important reservoirs of carbon in terrestrial ecosystems. Assessments of both SOC and SIC are lacking in arid regions. We carried out a survey in central Xinjiang, the Yanqi Basin, to evaluate the dynamics of SOC and SIC. Twenty-one soil profiles were sampled from three land types: desert, shrub and agricultural soils. We determined SOC and SIC and the stable carbon isotope compositions (δ13C). Our data showed a decrease with depth for SOC in all soil profiles but an increase for SIC except in the desert soils. Both SOC and SIC stocks (over the 0–30-cm depth) were least in the desert soils (1.0 ± 0.3 and 4.0 ± 0.8 kg C m−2 for SOC and SIC, respectively) but greatest in the agricultural soils (4.6 ± 0.6 and 11.0 ± 2.0 kg C m−2 for SOC and SIC, respectively). Total soil carbon stocks at 0–100 cm were 11.6 ± 4.8, 45.1 ± 10.4 and 51.2 ± 5.6 kg C m−2 in the desert soils, shrub soils and agricultural soils, respectively. On average, SIC accounted for more than 80% of the total carbon in this region. There were no significant differences in δ13C of SOC between land-use types. In contrast, the δ13C of SIC was different: desert soils (−0.6‰) > shrub soils (−2.2‰) > agricultural soils (−3.4‰). The depleted 13C in SIC in the agricultural soils indicates enhancement of pedogenic carbonate by cropping. Our study suggests that converting shrub land to agricultural land in arid regions may lead to an increase not only in SOC stock, but also in SIC stock.