Seawalls have increasingly been constructed to control the invasion of an exotic perennial grass, Spartina alterniflora, in coastal wetlands of eastern China. We investigated soil organic carbon (C) and nitrogen (N), available and microbial C and N, soil microbial community composition and biomass in a seawall-reclaimed S. alterniflora salt marsh compared with an adjacent natural S. alterniflora salt marsh. Seawall reclamation in S. alterniflora salt marsh significantly decreased soil salinity, moisture, litter and root biomass, and strongly decreased soil total organic C by 57% and total organic N by 59%, and also lowered soil available C and N in S. alterniflora salt marsh. Seawall reclamation significantly decreased soil microbial biomass C and the quantities of the total phospholipid fatty acids (PLFAs), and bacterial, fungal, gram-negative bacterial, gram-positive bacterial, saturated straight-chain, and monounsaturated PLFAs in deeper soil layers (10–30cm). Our results suggested that seawall construction could greatly decrease soil C and N accumulation of S. alterniflora salt marsh by decreasing S. alterniflora residuals input into the soil and lowering soil salinity and moisture, which further decreased soil microbial biomass by lowering soil available C and N in S. alterniflora salt marsh. Changes in soil microbial community composition and biomass could in turn affect soil C and N accumulation in a seawall-reclaimed S. alterniflora salt marsh in eastern China.