This study aims to better understand the underlying mechanisms of the coexistence of shrub and grass species in arid environments. A typical shrubgrass community, Nitraria tangutorum-Achnatherum splendens community, was selected near the Shahu Lake in Ningxia Hui Autonomous Region, Northwest China. To characterize the heterogeneity of the habitat, we partitioned the community into three microhabitats, namely under-canopy, transitional and open microhabitats, from the canopy areas of plant clumps to the inter-clump barren areas. With trenching methods, roots were collected and the distributions of root biomass densities and root extinction coefficients of the two species were compared in the soil profiles of the three microhabitats. The results showed that both Nitraria and Achnatherum produced most of their roots in under-canopy microhabitats; however, the extent of decline in root biomass density from undercanopy to open microhabitats was more intensive in Achnatherum. The layers with highest root biomass density of Nitraria were continuously deepened from undercanopy to open microhabitats, while that of Achnatherum re-increased in open microhabitats. Nitraria had its highest fine root biomass density in 10-30 cm layer in the undercanopy microhabitat, while the highest fine root biomass density of Achnatherum was in 0-10 cm layer. There were significant (or marginally significant) differences in root extinction coefficients between the two species in all microhabitats, indicating that there was belowground niche segregation between Nitraria and Achnatherum. Taking into account of the patchy clumpstyle aboveground distribution pattern, we suggest that aboveground aggregation together with belowground segregation might be the coexistence strategies of Nitraria and Achnatherum to cope with arid environments.