The invasion and expansion of Spartina alterniflora in coastal salt marsh wetlands have greatly affected the material cycle of the ecosystem. A total of 372 topsoil samples were collected from 124 sites representing two land-cover types by implementing an unprecedented high sampling density study in the Dafeng Milu National Nature Reserve. Classical statistics and geostatistics were used to quantify soil organic carbon (SOC) and total nitrogen (TN) spatial distribution. Redundancy analysis (RDA) was used to detect correlations between environmental factors, SOC, and TN. The results showed that SOC and TN have moderate variability. The spatial distributions of SOC and TN were similar, and the highest values were observed in the southwest of the study area. In different land cover types, the SOC and TN in the vegetation coverage areas with Spartina alterniflora as the dominant species were significantly higher than those in bare land. RDA showed that TN and aboveground biomass significantly affected the spatial distribution of SOC, while SOC and AGB dominated the spatial distribution of TN.