In the present study, soil microbial communities of mangrove forests and its responses to the invasion of Spartina alterniflora were analyzed using phospholipid fatty acid analysis (PLFA). Soil physic-chemical properties and enzyme activities were measured in the Minjiang River Estuary. The results showed that: There were 22 PLFAs that were significantly different in soil samples from mangrove communities (MC), Mangrove-S. alterniflora (MS), and S. alterniflora communities (SC). The MS soil exhibited richer PLFAs than the other vegetation types. The physic-chemical properties and enzyme activities in soils of different vegetation communities were in the order of MC > MS > SC. Following the invasion of S. alterniflora, the soil microbial biomass of mangrove communities increased, and the physic-chemical properties, enzyme activities significantly decreased, and the quality of mangrove wetland soil was degraded. The PLFAs biomarkers of three species with the highest contents were 16:0, 16:1w7c, 9Me15:0w, and 18:1w12c. There was a significant difference in the relative biomass of soil microbial biomass. Bacteria exhibited the richest distribution, followed by fungus, actinomycetes, and protozoans. Community diversity indices showed a similar pattern, MS soil microbial community diversity indexes were less than those of MC. The soil microbial community diversity indexes decreased following the invasion of S. alterniflora. Principal component analysis was able to distinguish the characteristics of microbial communities in different vegetation communities. The soil physic-chemical properties were closely correlated with enzyme activities, and SOC, TN, sucrose, and catalase were significantly correlated with the PLFAs of gram-positive bacteria and actinomycetes. The results of this study showed that the invasion of S. alterniflora has the potential to affect nutrient metabolism in the mangrove community, especially with regard to the C, N and P cycles, and the enzyme activities. S. alterniflora can change the microbial biomass to create favorable soil environments for their growth to achieve the rapid invasion.