Soil microorganisms play a key role on soil carbon (C) and nutrient cycling, which can serve as an indicator of the status of soil quality. Therefore, it is crucial to study the soil microbial community composition to understand the evolvement in soil quality owing to vegetation restoration. The aim of the study was to investigate the effect of the fern species Dicranopteris dichotoma on the soil microbial biomass and community structure. The typical sequence of vegetation restoration (Y0, without measures of ecological restoration; Y13, restoration for 13 years; Y31, restoration for 31 years) was selected as the research object in Hetian town, Changting county, Fujian province. At each experimental site, the soil was subjected to three treatments-NRd, not removed D. dichotoma; Rd, removed D. dichotoma; and CK, control. Our results indicated that soil microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and total phospholipid fatty acid(PLFAs) under CK treatment were significantly higher than those under NRd and Rd treatments. Soil MBC and total PLFAs decreased significantly (P < 0.05) after Rd treatment for 4 months, indicating that D. dichotoma had a significant effect on soil microbial biomass. PLFAs of Gram-positive and Gram-negative bacteria, arbuscular mycorrhizal fungi, fungi, actinomycetes under NRd treatment were significantly lower than those under CK treatment (except for Y13). The ratios of soil Gram-positive bacteria to Gram-negative bacteria, cyclopropyl to cyclopropyl precursor, and saturated straight chain fatty acid to monounsaturated fatty acids were significantly decreased under NRd treatment compared to those under CK treatment; however, the fungi to bacteria ratio was significantly increased under NRd treatment (P < 0.05), indicating that the soil microbial biomass and community structure was much more abundant under NRd treatment, and high microbial activity was also noted. The results of Pearson correlation analysis and Redundancy analysis suggested that the soil chemical and physical properties were significantly and positive related to the soil microbial biomass and community structure. Therefore, soil C:N ratio, pH, and N status are key factors that affect the soil microbial community in the red soil erosion area.