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Soil microorganisms can be altered by plant invasion into wetland ecosystems and comprise an important linkage between phosphorus (P) availability and soil carbon (C) chemistry; however, the intrinsic mechanisms of P and C transformation associated with microbial community and function are poorly understood in coastal wetland. In this study, we used a sequential fractionation method and 13C nuclear magnetic resonance (NMR) spectroscopy to capture the changes in soil P pools and C chemical composition with bare flats (BF), native Phragmites australis(PA), and invasive Spartina alterniflora(SA), respectively. The responses of the soil microbial community using phospholipid fatty acid (PLFA) profiling and function indicated by nine enzyme activities associated with C, nitrogen (N), and P cycles were also investigated. Compared to PA and BF, SA invasion significantly (P < 0.05) changed P pools and mainly increased the available P by 17.5 and 37.0%, respectively. The presence of the plants (SA and PA) significantly (P < 0.05) altered the soil C chemical composition mainly by affecting the aliphatic functional groups, resulting in a lower alkyl C/O-alkyl C ratio value. Compared to BF and SA, PA significantly (P < 0.05) increased arbuscular mycorrhizal fungi (AMF) abundance. Soil enzyme activity, especially for the P and C cycle enzymes, was also affected by plant species with the highest geometric mean enzyme and hydrolase activity for the PA zone. We also found that soil C compositions and P pools were associated with microbial community structure and enzyme activity, respectively. However, little interaction between C and P was found on either soil microbial composition or soil enzyme activity variation. Further, microbial community composition was tightly correlated with the soil P compared to soil C chemistry, while enzyme activity showed more response with soil C chemistry compared to soil P pool changes.