Soil respiration releases a major carbon flux back to atmosphere and thus plays an important role in global carbon cycling. Soil respiration is well known for its significant spatial variation in terrestrial ecosystems, especially in fragile ecosystems of arid land, where vegetation is distributed sparsely and the climate changes dramatically. In this study, soil respiration in three typical arid ecosystems: desert ecosystem (DE), desert-farmland transition ecosystem (TE) and farmland ecosystem (FE) in an arid area of northwestern China were studied for their spatial variations in 2012 and 2013. Along with soil respiration (SR), soil surface temperature (ST), soil moisture (SM) and soil electrical conductivity (ECb) were also recorded to investigate the spatial variations and the correlations among them. The results revealed that averaged soil respiration rate was much lower in DE than those in TE and FE. No single factor could adequately explain the variation of soil respiration, except a negative relationship between soil temperature and soil respiration in FE (P < 0.05). Geostatistical analysis showed that the spatial heterogeneity of soil respiration in DE was insignificant but notably in both TE and FE, especially in FE, which was mainly attributed to the different vegetation or soil moisture characteristics in the three ecosystems. The results obtained in this study will help to provide a better understanding on spatial variations of soil respiration and soil properties in arid ecosystems and also on macroscale carbon cycling evaluations.