Shrubs can create “fertile islands” with improved soil and microclimatic conditions surrounded by a low-nutrient matrix in arid and semi-arid areas. But the relationship of sandy-soil adapted shrubs ( Caragana microphylla and Salix gordejevii) with the structure of soil macro-faunal assemblages is largely unknown in Horqin Sand Land, Northern China. The environmental variables and soil macro-faunal community were investigated under shrubs and in the open spaces between shrubs in this study. Environmental parameters (soil water, temperature, pH, EC, total organic carbon and nitrogen) indicated a significant alteration of the soil environment under shrubs in comparison with that in the open spaces. Significantly larger shrub canopy size and greater height were found for S. gordejevii than for C. microphylla. The microhabitats under shrubs maintained significantly higher abundance, group richness and diversity of soil macro-faunal communities in comparison with those in the open spaces, with a higher abundance and group richness but lower diversity under the legume C. microphylla than under S. gordejevii. Further, data for the different faunal groups characterized specific responses to varying microhabitats under shrubs. Results implied that soil microhabitats under shrubs, in addition to shrub characteristics, could facilitate macro-fauna assemblages and diversity in shifting sand lands, which by feedback is beneficial for recovery, conservation and sustainable management in a sandy ecosystem.