Biological soil crusts (BSCs) are an important cover in arid desert landscapes, and have a profound effect on the CO2 exchange in the desert system. Although a large number of studies have focused on the CO2 flux at the soil–air interface, relatively few studies have examined the soil CO2 concentration in individual layers of the soil profile. In this study, the spatiotemporal dynamics of CO2 concentration throughout the soil profile under two typical BSCs (algae crusts and moss crusts) and its driving factors were examined in a revegetated sandy area of the Tengger Desert from Mar 2010 to Oct 2012. Our results showed that the mean values of the vertical soil CO2 concentrations under algal crusts and moss crusts were 600–1,200 μmol/mol at the 0–40 cm soil profiles and increased linearly with soil depth. Daily CO2 concentrations showed a single-peak curve and often had a 1–2 h time delay after the maximum soil temperature. During the rainy season, the mean soil CO2 concentration profile was 1,200–2,000 μmol/mol, which was 2–5 times higher as compared to the dry season (400–800 μmol/mol). Annually, soil moisture content was the key limiting factor of the soil CO2 concentration, but at the daily time scale, soil temperature was the main limiting factor. Combined with infiltration depth of crusted soils, we predicted that precipitation of 10–15 mm was the most effective driving factor in arid desert regions.