As one of the most sensitive regions to global climate change, alpine tundra in many places around the world has been undergoing dramatic changes in vegetation communities over the past few decades. Herbaceous plant species in the Changbai Mountains area have significantly expanded into tundra shrub communities over the past 30 yr. Soil microbial communities, enzyme activities, and soil nutrients are intertwined with this expansion process. In order to understand the responses of the soil microbial communities to such an expansion, we analyzed soil microbial community structures and enzyme activities in shrub tundra as well as areas with three different levels of herbaceous plant expansion. Our investigation was based on phospholipid fatty acid (PLFA) analysis and 96-well microtiter plates. The results showed that herbs have expanded greatly in the tundra, and they have become the dominant species in herbaceous plant expansion areas. There were differences for community composition and appearance among the shrub tundra and the mild expansion, moderate expansion, and severe expansion areas. Except for soil organic matter, soil nutrients were increased in herbaceous plant expansion areas, and the total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), and available phosphorus (AP) were greatest in moderate expansion areas (MOE), while soil organic matter levels were highest in the non-expanded areas (CK). The total soil PLFAs in the three levels of herbaceous plant expansion areas were significantly higher than those in the non-expanded areas, and total soil PLFAs were highest in the moderately expanded area and lowest in the severely expanded area (SEE). Bacteria increased significantly more than fungi and actinomycetes with herbaceous plant expansion. Soil hydrolase activities (β-1,4-glucosidase (βG) activity, β-1, 4-N-acetylglucosaminidase (NAG) activity, and acid phosphatase (aP) activity) were highest in MOE and lowest in the CK treatment. Soil oxidase activities (polyphenol oxidase (PPO) activities and peroxidase (PER) activities) were also highest in MOE, but they were lowest in the SEE treatment. The variations in total soil PLFAs with herbaceous plant expansion were mostly correlated with soil organic matter and available phosphorus concentrations, while soil enzyme activities were mostly correlated with the total soil nitrogen concentration. Our results suggest that herbaceous plant expansion increase the total soil PLFAs and soil enzyme activities and improved soil nutrients. However, soil microorganisms, enzyme activity, and nutrients responded differently to levels of herbaceous plant expansion. The soil conditions in mild and moderate expansion areas are more favorable than those in severe expansion areas.