Background: Community structure and species composition are closely related to plant diversity and ecosystem stability. To explore the similarity in vegetation structure of shrub communities under the same temperate climate but with different microhabitats, 36, 28 and 13 sampling plots in Ephedra distachya, Seriphidium terrae-albae and Artemisia songarica communities were selected respectively, during the course of three seasons (early spring, summer, autumn) in Gurbantunggut Desert, north-western China. The species composition, abundance, biomass and soil nutrients were investigated. Floristic changes were characterized by similarity and ordination methods. Results: Two communities, E. distachya and S. terrae-albae, were similar in terms of soil nutrients but differed from the A. songarica community. Soil organic matter, nitrogen and biological soil crusts accounted for the differences of microhabitats. In spring and summer, more plant families, genera and species were recorded in E. distachya and S. terrae-albae communities than in the A. songarica community but in each community, the number of families, genera, species, herbs and life forms showed a consistent trend summer > spring > autumn. There were significant differences in absolute biomass among the three communities, but the ratio of dead biomass to total biomass was consistently 1:4, indicating the constant turnover rate of plant biomass for nutrient cycling. In each community shrubs accounted for the most biomass. Herbaceous biomass was negligible but the herbs contributed the most richness and abundance. Conclusions: The similarity in response of all three communities to seasonal changes in vegetation structure and biomass allocation demonstrate convergence although divergence is demonstrated in soil characteristics or microhabitats.