Understanding the factors that drive variation in species distribution is a central theme of ecological research. Although several studies focused on alpine vegetation, few efforts have been made to identify the environmental factors that are responsible for the variations in species composition and richness of alpine shrublands using numerical methods. In the present study, we investigated vegetation and associated environmental variables from 45 sample plots in the middle Qilian Mountains of the northwestern China to classify different community types and to elucidate the species-environment relationships. We also estimated the relative contributions of topography and site conditions to spatial distribution patterns of the shrub communities using the variation partitioning. The results showed that four shrub community types were identified and striking differences in floristic composition were found among them. Species composition greatly depended on elevation, slope, shrub cover, soil pH and organic carbon. The important determinants of species richness were soil bulk density and slope. No significant differences in species richness were detected among the community types. Topography and site conditions had almost equal effects on compositional variation. Nonetheless, a large amount of the variation in species composition remained unexplained.