In order to elucidate the activity and ecological distribution of arbuscular mycorrhizal (AM) fungi in Saibei desert steppe, we sampled soil from three different sites at Erniudian,Shangduzhen and Qinggeletu in Saibei desert steppe in June 2013. Roots of Caragana korshinskii and rhizosphere soil were collected from each site at five depths in the soil profile: 0-10, 10-20, 20-30, 30-40 and 40-50 cm, respectively. The results indicated that C. korshinskii formed strong symbiotic relationship with AM fungi. AM fungal spore density and colonization rates were significantly affected by sampling sites and soil depths. The highest spore density occurred at the 0-10cm layer and gradually decreased with soil depths. Hyphal colonization rate was the highest in samples collected at Shangduzhen among the three sites. However, vesicular colonization was the lowest in samples from Qinggeletu, and there were no significant differences among soil layers. Arbuscular colonization differed among the three sites. Both the total colonization rates and colonization intensity of AM fungi in root samples from Shangduzhen were the highest compared to the other two sites, respectively. Spore density strongly correlated with soil organic C, total N, easily extractable glomain (EEG) and total extractable glomalin (TG) (all P<0.01), soil pH (P<0.05), and negatively correlated with available P (P<0.01). Hyphal colonization rate had negative correlation with soil pH, available P, total N and acid phosphatase (all P<0.05). Vesicular and arbuscular colonization rates were strongly correlated with available N and alkaline phosphatase (all P<0.01). EEG and TG had significant positive correlation with available N, total N, alkaline phosphatase and acid phosphatase (all P<0.01), urease (P<0.05), but had no significant correlation with available P. Principal component analysis showed that acid and alkaline phosphatase, TG, total N and organic carbon were the key factors affecting soil nutrient status. The average contents of TG and EEG were 3.19 mg/g and 1.17 mg/g accounting for 7.77% and 3.83% of the total soil organic carbon, and 20.81% and 9.57% of the total soil nitrogen, respectively. Multiple linear regression analysis showed significant linear correlation between TG or EEG and soil organic C and total N, respectively. The results suggest that AM fungal colonization and glomalin are useful indicators for evaluating soil quality and function of desert ecosystem on the basis of its relationship with AM fungal distribution, soil nutrient dynamics, carbon and nitrogen cycle.