The Changbai Mountain is a mountainous ecosystem strongly affected by volcanic eruptions and with distinct vegetation zonations along different altitudes. This region offers a natural laboratory for studying post-volcanic ecosystem reconstruction and forest succession. Owing to the existence of elevation change in the vertical direction, ecological factors in mountainous ecosystems occur in a series of changes over a relatively small space. Therefore, mountainous ecosystems have become an important area to study correlation mechanisms among soil microbes, enzyme activities, and ecological factors. The objectives of the present study were to:(1) examine the distribution of microbial phospholipid fatty acids (PLFA) and enzyme activities of soils along different altitudes of Changbai Mountain and investigate factors affecting the PLFA and enzymes, and (2) explore the effects of influencing factors, vegetation, and soil on the microbial community structure and enzyme activities in four vertical zones. We sampled soils in the coniferous forest zone, ermans birch forest zone, alpine meadow zone, and alpine tundra zone along the altitudinal gradient. We determined soil microbial community structure with the PLFA method and enzyme activities with the microplate method. The results demonstrated that three environmental factors, the concentration of soil organic carbon, total nitrogen (TN), and total phosphorus increased and then decreased as elevation increased. Soil organic carbon and TN varied with altitude, with the highest value detected in the ermans birch forest zone. Both the total microbial PLFA and various types of microbes PLFA initially increased and then decreased as elevation increased. The rank of the PLFA amount was ermans birch forest zone > coniferous forest zone > alpine meadow zone > alpine tundra zone. The rank of the contribution rate of total microbial PLFA was bacteria > fungi > actinomycetes, and Gram-negative bacteria (G^-) > Gram-positive bacteria (G⁺). In terms of microbial PLFA correlation, bacteria, actinomycetes, Gram-positive bacteria (G⁺), and Gram-negative bacteria (G^-) were significantly correlated, while fungi was poorly correlated with these microbes. TN showed a significant positive correlation with various types of microbes while the C/N ratio was negatively correlated with various types of microbes. Thus, it can be seen that TN and C/N ratio were the two main factors differentiating soil microbial community structure along the altitudinal gradient. Both soil β-glucosidase and acid phosphatase (AP) activities increased with increased elevation. The AP activity showed high response to the alpine tundra ecosystem. Soil water content, soil organic carbon, and C/N ratio were the main factors affecting the vertical distribution of soil enzyme activities. The meadow processes of alpine tundra strongly affected the soil water content, soil total phosphorus, and AP activity; however, had little effect on soil microbial PLFA and other enzyme activities. In conclusion, the soils microbial community structure and enzyme activities along different altitudes of Changbai Mountain were not only affected by soil environmental factors and hydrothermal conditions, but were also closely related to the vegetation community composition and litter chemical quality.