To understand the impacts of altitude change on soil microbial community in mountain forest in arid region, and to reveal the structural characteristics and influencing factors of soil microbial community after environmental factors change. In this study, the physicochemical properties of soil were measured at five altitudinal gradients in Helan Mountain, and the composition of soil microbial community was determined using phospholipid fatty acids (PLFA) spectrum analysis. The correlation between soil physicochemical properties and the abundance of soil microbial community was explored by principal component analysis and redundancy analysis. The results showed that soil nutrients were significant difference at different altitudes (P < 0.05). The content of soil organic carbon and total nitrogen increased with the increase of altitude. The total phosphorus content increased first, then decreased and increased with altitude. The content of soil microorganism first increased and then decreased with altitude, and the abundance of soil microorganism was significant difference among different altitudes (P < 0.05). Principal component analysis showed that the microbial groups, which play a major role on first principal component, were gram-positive bacteria (G⁺), gram-negative bacteria (G^-) and fungi, and which play a major role on second principal component, were actinomycetes, protozoa and non-specific bacteria. Non-specific bacteria and fungi had significant correlation with soil factors, actinomycetes, G⁺ and G^- bacteria had weak correlation with soil factors, while protozoa had close relationship with soil total phosphorus content. Altitude was an important factor affecting the distribution of characteristic microorganisms. The content and abundance of characteristic microorganisms first increased and then decreased with the increase of altitude, which basically accorded with the theory of "central expansion" in mountain ecology. This study explored the relationship between soil microbial structure characteristics and soil physicochemical properties at different altitudes in Helan Mountain, which is great significance for maintaining the functional stability and nutrient cycle of mountain forest ecosystem in arid areas.