Soil respiration is one of the most sensitive ecosystem processes to climate change, but is little known in desert ecosystems. The spatial and temporal changes in soil respiration directly influence the local and regional carbon budgets. In order to understand the controlling factors of soil respiration in desert ecosystem, we selected Xiaotang, in the northern margin of the Taklimakan Desert, as a site to analyze daily variation of soil respiration and its relationship with soil temperature and soil water content for two soil types (saline-alkali land and shifting sandy land). Soil respiration was measured by a LI-8150 soil CO² efflux system from 21 January to 31 January in 2013. The observation indicated that: (1) Soil respiration rates for the two types of soil were relatively slow, but showed obvious diurnal patterns, which displayed a single peak curve with the maximum rate occurring between 13:00-15:00. (2) On nights, most of the soil respirations were negative at the two types of soil, which indicated that soil had evident carbon sink functions. But in days, the desert soil was a weak carbon source. (3) The daily variation trends of soil respiration rates were fairly consistent with soil temperature at 0-5 cm depth for the two types of soil. Linear and exponential model could effectively describe the relationship between soil respiration rate and soil temperature at 0-5 cm depth in saline-alkali land and shifting sandy land, respectively. The Q₁₀ values for the two types of soil were kept at a lower level, among them the Q₁₀ values of saline-alkali land was relatively larger. (4) There was a significant linear relationship between soil respiration rate and soil water contents at 0-5 cm depth. (5) Two-dimensional regression of soil temperature and soil water content could better explain daily variation of soil respiration than one single factor regression. Moreover, the soil temperature and soil water content on soil respiration rate were respectively showed the significant hysteresis effect.