The study of elevational diversity gradients dates back to the foundation of biogeography. Elevational diversity patterns on plant and animal taxa have been studied exclusively over the past century, however, pattern of soil microbial diversity along an elevation gradient remain poorly understood, especially in the arid sand areas. Helan Mountain is one of few well conserved natural ecosystems in North-West of China, which have the characteristic of the significant vertical distribution of vegetation and the vegetation horizontal zonation from desert to frigid zones. Therefore, it will provide us an idea study model to assess the generality of elevational diversity patterns for soil bacterial diversity along an elevation gradient. Here, we present a comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from desert steppe to subalpine meadow. The structure and function of soil microbial community were studied by using Biolog plate and phospholipid fatty acid methyl ester (FAMEs), respectively. The results showed that soil microbial functional diversity and community structure differed significantly along the elevation gradient (vegetation types). Shannon-Weiner index (H) of soil microbe and species evenness index (E) showed an increasing trend (P < 0.05). The order of microbial metabolic activity was subalpine meadow > cold temperate coniferous forest > coniferous mixed forest > temperate coniferous forest > arid dwarf-scrub > desert steppe, thus the maximal microbial metabolic activity would alter soil C and N cycling to meet available nutrients for plants in the high altitude sites, because soil N and P increased with the elevation The FAMEs analysis showed that micro flora shifted along the elevational gradient and soil bacteria dominated microbial community, however, differed significantly along the elevation gradient (vegetation types). Soil microbial diversity and number and type of phospholipid fatty acid biomarkers were the highest in the cold temperate coniferous forest. The relative contents of phospholipid fatty acid in bacteria, fungi were also the highest in the cold temperate coniferous forest. The order of microbial community diversity was cold temperate coniferous forest > coniferous mixed forest > temperate coniferous forest > subalpine meadow > mountain xerophytic shrub > desert steppe, which indicated that more litter or organic resource in forest ecosystems than grasslands would favor soil microbial diversity. These results supported that microbes do not follow the elevational diversity patterns of plants and the difference could be caused by ecological and evolutionary processes across the gradient. The finding suggests that there were more suitable microorganisms, which played more important in maintaining ecosystem stability in the arid sand areas.