Soil microorganisms play an important role for maintaining the functional stability of forest ecosystem in arid areas. However, distribution of soil microbial community structure and diversity along an elevation gradient remains poorly understood, especially in the arid areas. In this study, the phospholipid fatty acid analysis (PLFA) was used to examine variations in soil microbial community diversity along an elevational eastern slope in the Helan Mountain (Desert Steppe (HM), Amygdalus mongolica (Maxim) Ricker (MG), Pinus tabulaeformis forest (YS), Mixed forest (HJ), Picea crassifolia Kom forest(QH)). The results showed that, there existed 59 PLFAs which were significantly different in the soil samples from different vegetation types. The YS soil exhibited richer PLFAs distribution amount than the other vegetation types. The PLFAs biomarkers of five vegetation types with the highest contents were 16:0, 18:1ω9c, 18:1ω7c, 10Me 16:0 and 18:2ω6c, respectively. The amount of characteristic microorganisms was different in soil of different vegetation types, the bacteria had the richest distribution, followed by fungi, actinomycetes and protozoa. Cluster analysis showed that soil PLFAs could be divided into different groups in different vegetation types, 16:0, 18:1ω9c and 18:1ω7c could be divided into one group in different vegetation types. The heat map of the common PLFAs in different vegetation types was drawn. It was found that the distribution of different PLFAs was different in different vegetation types, and the distribution of PLFAs in YS vegetation was the highest. The diversity of soil microbial communities in different vegetation types showed that the microbial diversity index in HJ was higher than the other vegetation types, and the HM was the lowest, indicating that soil microbial diversity was closely related to vegetation diversity. Component analysis (PCA) identified 2 principal component factors in relation to microbial community diversity, explaining 78.01% and 8.80% of the variation, respectively. The microorganisms, which play a major role on first principal component, are nonspecific bacteria; Gram-positive bacteria and Gram-negative bacteria, fungi, actinomycetes and protozoa, which play a major role on second principal component, are anaerobic bacteria. Correlation analysis between soil microorganisms and soil factors showed that soil organic carbon (SOC) and total nitrogen (TN) were positively correlated with soil microbial groups and diversity index, while pH and bulk density (BD) were negatively correlated with microbial groups and diversity index. The change of soil factors caused by altitude was an important factor affecting soil microbial community structure and diversity. The results show that YS soil has the highest microbial content, and HJ soil has the highest microbial diversity, which accords with the theory of high biodiversity in the central region of mountain ecosystem, and can provide scientific basis for the study of soil microorganisms and the management of Helan Mountain Nature Reserve.